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<h3>
Andreas Tille pushed to branch master
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/46dd21e29ae2b360ca730fc6f67ecd45ea321a51">46dd21e2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-19T08:23:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.7.1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/14ce137813eb6ec29204e58ee43533653d08ae59">14ce1378</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-19T08:23:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/d0b0b374c399cf1b7480109cae576b8b0eb263a4">d0b0b374</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-19T08:23:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.7.1'
Update to upstream version '0.7.1'
with Debian dir 28a6471fb462470d93e614097b750dca4739742c</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/0f3b72fc4ed67d190b1f3eea27f380deee9aaec7">0f3b72fc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-19T08:24:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#899ce9c202bf7bb5480e72836c3edc773c9c4244">
.github/workflows/ci.yml
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<li class="file-stats">
<a href="#4990be809a537bf86e4be2fe2e8251c83d8bd129">
CHANGES.rst
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">
pyproject.toml
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<li class="file-stats">
<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
<span class="new-file">
+
setup.cfg
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</a>
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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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="#b31d13e8151f786e577da1e989935f7ba967c4e8">
src/dnaio/chunks.py
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<li class="file-stats">
<a href="#a66e9807f4b39aaa61baab58ad1a281bd6691999">
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">
src/dnaio/singleend.py
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</li>
<li class="file-stats">
<a href="#ac9c6701e83ec81d3f6fff83e5237d3f8bcb18c2">
tests/test_chunks.py
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<li class="file-stats">
<a href="#307d17476eda4102236d69ec93ead958067e02d6">
tests/test_internal.py
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<li class="file-stats">
<a href="#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c">
tox.ini
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</ul>
<h4>Changes:</h4>
<li id="899ce9c202bf7bb5480e72836c3edc773c9c4244">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#899ce9c202bf7bb5480e72836c3edc773c9c4244"><strong>.github/workflows/ci.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ on: [push, pull_request]</td>
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<td class="old_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">
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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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"></span>
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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">
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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">
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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="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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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">
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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">
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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="yaml"> <span class="na" style="color: #008080;">lint</span><span class="pi">:</span></span>
</pre>
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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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">5</span></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="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">
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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="yaml"> <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">10</span></span></span>
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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">
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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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
</pre>
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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">
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="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="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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,62 +16,89 @@ jobs:</td>
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<td class="old_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="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>
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<td class="old_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="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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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">
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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">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.python-version }}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install <span class="idiff left right">dependencies</span></span></span>
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<td class="old_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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<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">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install <span class="idiff left right">tox</span></span></span>
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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="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">python -m pip install tox</span></span>
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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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Run tox ${{ matrix.toxenv }}</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">tox -e ${{ matrix.toxenv }}</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">fetch-depth</span><span class="pi">:</span> <span class="m" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># required for setuptools_scm</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build sdist and temporary wheel</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">pipx run build</span></span>
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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;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/upload-artifact@v2</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">sdist</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">dist/*.tar.gz</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"></span>
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24
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">5</span></span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">10</span></span></span>
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26
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<pre style="margin: 0;"> <span id="LC39" 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>
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27
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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28
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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29
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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 class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.10-dev"</span><span class="pi">]</span></span>
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30
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42
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<pre style="margin: 0;"> <span id="LC42" 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>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="pi">[</span><span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span><span class="pi">,</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span><span class="pi">,</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span><span class="pi">,</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.9"</span><span class="pi">,</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.10"</span><span class="pi">]</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="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>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">macos-latest</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">macos-latest</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">windows-latest</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up Python ${{ matrix.python-version }}</span></span>
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37
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.python-version }}</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install <span class="idiff left right">dependencies</span></span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install <span class="idiff left right">tox</span></span></span>
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41
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">python -m pip install tox</span></span>
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42
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test</span></span>
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43
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">tox -e py</span></span>
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44
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Upload coverage report</span></span>
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<td class="old_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">
45
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">codecov/codecov-action@v1</span></span>
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46
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="yaml"></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">deploy</span><span class="pi">:</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;">5</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml"> <span class="na" style="color: #008080;">wheels</span><span class="pi">:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">github.event_name == 'push' && startsWith(github.ref, 'refs/tags')</span></span>
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50
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="yaml"> <span class="na" style="color: #008080;">needs</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">lint</span><span class="pi">,</span> <span class="nv" style="color: #008080;">test</span><span class="pi">]</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">startsWith(github.ref, 'refs/tags')</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;">15</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" 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-20.04</span><span class="pi">,</span> <span class="nv" style="color: #008080;">windows-2019</span><span class="pi">]</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" 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>
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52
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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53
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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54
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="yaml"> <span class="na" style="color: #008080;">fetch-depth</span><span class="pi">:</span> <span class="m" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># required for setuptools_scm</span></span>
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56
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build wheels</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypa/cibuildwheel@v2.1.1</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="yaml"> <span class="na" style="color: #008080;">output-dir</span><span class="pi">:</span> <span class="s" style="color: #d14;">dist/</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypa/cibuildwheel@v2.1.2</span></span>
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60
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_BUILD</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">cp3*-manylinux_x86_64"</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_MANYLINUX_X86_64_IMAGE</span><span class="pi">:</span> <span class="s" style="color: #d14;">manylinux2010</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_BUILD</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">cp*-manylinux_x86_64</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">cp3*-win_amd64"</span></span>
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63
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_ENVIRONMENT</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">CFLAGS=-g0"</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up Python</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_TEST_REQUIRES</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pytest"</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_TEST_COMMAND_LINUX</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">cd</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">{project}</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">pytest</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">tests"</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_TEST_COMMAND_WINDOWS</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">cd</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">/d</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">{project}</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">&&</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">pytest</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">tests"</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/upload-artifact@v2</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">wheels</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">wheelhouse/*.whl</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="yaml"> <span class="na" style="color: #008080;">publish</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">github.event_name == 'push' && startsWith(github.ref, 'refs/tags')</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="yaml"> <span class="na" style="color: #008080;">needs</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">build</span><span class="pi">,</span> <span class="nv" style="color: #008080;">wheels</span><span class="pi">]</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/download-artifact@v2</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">sdist</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">dist/</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/download-artifact@v2</span></span>
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66
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.7</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Make distributions</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m pip install build</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m build --sdist</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="yaml"> <span class="s" style="color: #d14;">ls -l dist/</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">wheels</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">dist/</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Publish to PyPI</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypa/gh-action-pypi-publish@v1.4.<span class="idiff left right">1</span></span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypa/gh-action-pypi-publish@v1.4.<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="yaml"> <span class="na" style="color: #008080;">user</span><span class="pi">:</span> <span class="s" style="color: #d14;">__token__</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="yaml"> <span class="na" style="color: #008080;">password</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.pypi_password }}</span></span>
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<li id="4990be809a537bf86e4be2fe2e8251c83d8bd129">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#4990be809a537bf86e4be2fe2e8251c83d8bd129"><strong>CHANGES.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,17 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Changelog</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">=========</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">v0.7.1 (2022-01-26)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">-------------------</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">* PR #34: Fix parsing of FASTA files that just contain a comment and no reads</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">v0.7.0 (2022-01-17)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">-------------------</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">* @rhpvorderman contributed many performance improvements in PR #15, #17, #18, #20, #21, #22, #23. Reading and writing FASTQ files and reading of paired-end FASTQ files was sped up significantly. For example, reading uncompressed FASTQ is 50% faster (!) than before.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">* PR #28: Windows support added</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">v0.6.0 (2021-09-28)</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">-------------------</span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-dnaio (0.7.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 19 Feb 2022 08:23:26 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">python-dnaio (0.6.0-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491"><strong>pyproject.toml</strong></a>
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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>
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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>
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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 >= 45"</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 >= 6.2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Cython >= 0.29.20"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="toml"><span class="py">build-backend</span> <span class="p">=</span> <span class="s" style="color: #d14;">"setuptools.build_meta"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="toml"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="toml"><span class="nn" style="color: #555;">[black.tool]</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="toml"><span class="py">line-length</span> <span class="p">=</span> <span class="mi" style="color: #099;">100</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="toml"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="toml"><span class="nn" style="color: #555;">[tool.setuptools_scm]</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="toml"><span class="py">write_to</span> <span class="p">=</span> <span class="s" style="color: #d14;">"src/dnaio/_version.py"</span></span></pre>
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<li id="8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[metadata]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">name = dnaio</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">author = Marcel Martin</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">author_email = marcel.martin@scilifelab.se</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">url = https://github.com/marcelm/dnaio/</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">description = Read and write FASTA and FASTQ files efficiently</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">long_description = file: README.md</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">long_description_content_type = text/markdown</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">license = MIT</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">classifiers =</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Development Status :: 5 - Production/Stable</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Intended Audience :: Science/Research</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> License :: OSI Approved :: MIT License</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Programming Language :: Cython</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Programming Language :: Python :: 3</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Topic :: Scientific/Engineering :: Bio-Informatics</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">[options]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">python_requires = >=3.6</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">package_dir =</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> =src</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">packages = find:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">install_requires =</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> xopen >= 1.4.0</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">[options.packages.find]</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">where = src</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">[options.package_data]</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">* = py.typed, *.pyi</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">[options.extras_require]</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">dev =</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> Cython</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> pytest</span></pre>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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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>
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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;">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>
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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;">distutils.command.sdist</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sdist</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.command.build_ext</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">build_ext</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">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>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"> <span class="s" style="color: #d14;">"""Change .pyx to .c or .cpp (copied from Cython documentation)"""</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">extension</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extensions</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">sources</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sfile</span> <span class="ow" style="font-weight: 600;">in</span> <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>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">path</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;">sfile</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC13" 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;">'.pyx'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.py'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extension</span><span class="p">.</span><span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'c++'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.cpp'</span></span>
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<pre style="margin: 0;">-<span id="LC16" 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="LC17" class="line" lang="python"> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.c'</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">sfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ext</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">sources</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">sfile</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">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>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">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>
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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>
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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>
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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>
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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>
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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>
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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;">self</span><span class="p">.</span><span class="n" style="color: #333;">extensions</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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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>
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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>
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<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;">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="LC34" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cythonize</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">extensions</span><span class="p">)</span></span>
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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>
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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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<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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<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="LC42" class="line" lang="python"> <span class="n" style="color: #333;">cythonize</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">distribution</span><span class="p">.</span><span class="n" style="color: #333;">ext_modules</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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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'README.md'</span><span class="p">,</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC47" 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;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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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;">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>
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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;">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="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">setuptools_scm</span> <span class="c1" style="color: #998; font-style: italic;"># noqa Ensure it’s installed</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'dnaio'</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;">setup_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'setuptools_scm'</span><span class="p">],</span> <span class="c1" style="color: #998; font-style: italic;"># Support pip versions that don't know about pyproject.toml</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">use_scm_version</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'write_to'</span><span class="p">:</span> <span class="s" style="color: #d14;">'src/dnaio/_version.py'</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">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="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 and write FASTA and FASTQ files efficiently'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">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>
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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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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="s" style="color: #d14;">'src'</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;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(</span><span class="s" style="color: #d14;">'src'</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"dnaio"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"py.typed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"*.pyi"</span><span class="p">]},</span></span>
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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="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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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: 5 - Production/Stable"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Science/Research"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">"License :: OSI Approved :: MIT License"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">"Natural Language :: English"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Cython"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="s" style="color: #d14;">"Programming Language :: Python :: 3"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Scientific/Engineering :: Bio-Informatics"</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC6" 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;">cythonize</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">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="LC9" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="p">),</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="p">)</span></span></pre>
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<li id="72ff21bf4040f97f9c5919d676e807b4117d01b7">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#72ff21bf4040f97f9c5919d676e807b4117d01b7"><strong>src/dnaio/_core.pyx</strong></a>
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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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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cython"></span>
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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>
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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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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 class="p">,</span> <span class="n" style="color: #333;">PyBytes_GET_SIZE</span></span>
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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;">cpython.unicode</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">PyUnicode_DecodeLatin1</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" 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 class="p">,</span> <span class="n" style="color: #333;">memchr</span><span class="p">,</span> <span class="n" style="color: #333;">strcspn</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cython"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cpython.unicode</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">PyUnicode_GET_LENGTH</span></span>
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<pre style="margin: 0;"> <span id="LC7" 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="LC8" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">extern</span> <span class="k" style="font-weight: 600;">from</span> <span class="o" style="font-weight: 600;">*</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">PyUnicode_1BYTE_DATA</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">object</span> <span class="n" style="color: #333;">o</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">PyUnicode_KIND</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">object</span> <span class="n" style="color: #333;">o</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">PyUnicode_1BYTE_KIND</span></span>
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<pre style="margin: 0;"> <span id="LC13" 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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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cython"><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>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cython"></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">@@ -34,11 +40,13 @@ cdef class Sequence:</td>
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<pre style="margin: 0;"> <span id="LC40" 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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cython"> <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="n" style="color: #333;">qualities</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;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">str</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">str</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">str</span> <span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># __cinit__ is called first and sets all the variables.</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</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="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">qualities</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;">sequence</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cython"> <span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">shorten</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="LC47" class="line" lang="cython"> <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;">"In read named {!r}: length of quality sequence "</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cython"> <span class="s" style="color: #d14;">"({}) and length of read ({}) do not match"</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="LC41" class="line" lang="cython"> <span class="idiff left right"> </span><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="LC48" class="line" lang="cython"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">"({}) and length of read ({}) do not match"</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="LC49" 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="LC50" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC51" 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="LC52" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</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">@@ -88,62 +96,91 @@ cdef class Sequence:</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cython"><span class="s" style="color: #d14;"> This is a faster version of qualities.encode('ascii')."""</span></span>
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<pre style="margin: 0;"> <span id="LC97" 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>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cython"></span>
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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="LC99" 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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">two_headers</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cython"> <span class="s" style="color: #d14;">"""Return the entire FASTQ record as bytes which can be written</span></span>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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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>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cython"></span>
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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>
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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>
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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>
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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>
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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>
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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>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cython"><span class="s" style="color: #d14;"> into a file.</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cython"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cython"><span class="s" style="color: #d14;"> Optionally the header (after the @) can be repeated on the third line</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cython"><span class="s" style="color: #d14;"> (after the +), when two_headers is enabled."""</span></span>
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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="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">name</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequence</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qualities</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">name_length</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">sequence_length</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">qualities_length</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cython"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">PyUnicode_KIND</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="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PyUnicode_1BYTE_KIND</span><span class="p">:</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cython"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #900; font-weight: 600;">PyUnicode_1BYTE_DATA</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>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cython"> <span class="n" style="color: #333;">name_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="nf" style="color: #900; font-weight: 600;">PyUnicode_GET_LENGTH</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>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Allow non-ASCII in name</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cython"> <span class="n" style="color: #333;">name_bytes</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;">'latin-1'</span><span class="p">)</span></span>
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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="cython"> <span class="n" style="color: #333;">name</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_bytes</span><span class="p">)</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cython"> <span class="n" style="color: #333;">name_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">PyBytes_GET_SIZE</span><span class="p">(</span><span class="n" style="color: #333;">name_bytes</span><span class="p">)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">PyUnicode_KIND</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="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PyUnicode_1BYTE_KIND</span><span class="p">:</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cython"> <span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #900; font-weight: 600;">PyUnicode_1BYTE_DATA</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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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="nf" style="color: #900; font-weight: 600;">PyUnicode_GET_LENGTH</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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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cython"> <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 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="c1" style="color: #998; font-style: italic;"># Don't allow non-ASCII in sequence and qualities</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_bytes</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>
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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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cython"> <span class="n" style="color: #333;">sequence</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_bytes</span><span class="p">)</span></span>
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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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">PyBytes_GET_SIZE</span><span class="p">(</span><span class="n" style="color: #333;">sequence_bytes</span><span class="p">)</span></span>
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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="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">PyUnicode_KIND</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 class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PyUnicode_1BYTE_KIND</span><span class="p">:</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cython"> <span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #900; font-weight: 600;">PyUnicode_1BYTE_DATA</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>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cython"> <span class="n" style="color: #333;">qualities_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="nf" style="color: #900; font-weight: 600;">PyUnicode_GET_LENGTH</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>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cython"> <span class="n" style="color: #333;">qualities_bytes</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>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cython"> <span class="n" style="color: #333;">qualities</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_bytes</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cython"> <span class="n" style="color: #333;">qualities_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">PyBytes_GET_SIZE</span><span class="p">(</span><span class="n" style="color: #333;">qualities_bytes</span><span class="p">)</span></span>
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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="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">create_fastq_record</span><span class="p">(</span><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>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cython"> <span class="n" style="color: #333;">name_length</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_length</span><span class="p">,</span> <span class="n" style="color: #333;">qualities_length</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cython"> <span class="n" style="color: #333;">two_headers</span><span class="p">)</span></span>
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114
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cython"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" 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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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" 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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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cython"><span class="s" style="color: #d14;"> repeated on the third line.</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" 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;">fastq_bytes</span><span class="p">(</span><span class="n" style="color: #333;">two_headers</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cython"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cython"></span>
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148
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<pre style="margin: 0;">+<span id="LC148" 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="nf" style="color: #900; font-weight: 600;">create_fastq_record</span><span class="p">(</span><span class="n" style="color: #333;">char</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;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qualities</span><span class="p">,</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">name_length</span><span class="p">,</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">sequence_length</span><span class="p">,</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">qualities_length</span><span class="p">,</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="n" style="color: #333;">two_headers</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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115
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153
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<pre style="margin: 0;"> <span id="LC153" 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>
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116
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># '@' to be put in front of the name.</span></span>
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117
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155
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<pre style="margin: 0;"> <span id="LC155" 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>
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118
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cython"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">two_headers</span><span class="p">:</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># We need space for the name after the +.</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cython"> <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>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cython"></span>
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119
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161
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<pre style="margin: 0;"> <span id="LC161" 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>
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120
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162
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<pre style="margin: 0;"> <span id="LC162" 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>
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121
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163
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<pre style="margin: 0;"> <span id="LC163" 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>
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122
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cython"></span>
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123
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165
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<pre style="margin: 0;"> <span id="LC165" 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>
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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;"><span class="idiff left right">Py_s</span>size_t</span> <span class="n" style="color: #333;">cursor</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">cursor</span></span>
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125
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167
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<pre style="margin: 0;"> <span id="LC167" 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>
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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<span class="idiff left right">_ptr</span></span><span class="p">,</span> <span class="n" style="color: #333;">name_length</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" 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</span><span class="p">,</span> <span class="n" style="color: #333;">name_length</span><span class="p">)</span></span>
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127
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169
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<pre style="margin: 0;"> <span id="LC169" 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>
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128
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170
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<pre style="margin: 0;"> <span id="LC170" 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>
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129
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<td class="new_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">
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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<span class="idiff left right">_ptr</span></span><span class="p">,</span> <span class="n" style="color: #333;">sequence_length</span><span class="p">)</span></span>
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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="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</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_length</span><span class="p">)</span></span>
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130
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172
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<pre style="margin: 0;"> <span id="LC172" 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>
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131
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173
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<pre style="margin: 0;"> <span id="LC173" 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>
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132
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174
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<pre style="margin: 0;"> <span id="LC174" 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>
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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="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">two_headers</span><span class="p">:</span></span>
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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="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;">name</span><span class="p">,</span> <span class="n" style="color: #333;">name_length</span><span class="p">)</span></span>
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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="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>
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133
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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
178
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<pre style="margin: 0;"> <span id="LC178" 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>
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134
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<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<span class="idiff left right">_ptr</span></span><span class="p">,</span> <span class="n" style="color: #333;">qualities_length</span><span class="p">)</span></span>
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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="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</span><span class="p">,</span> <span class="n" style="color: #333;">qualities_length</span><span class="p">)</span></span>
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135
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180
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<pre style="margin: 0;"> <span id="LC180" 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>
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136
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181
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<pre style="margin: 0;"> <span id="LC181" 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>
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137
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">retval</span></span>
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138
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cython"></span>
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139
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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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140
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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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141
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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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142
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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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143
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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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144
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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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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cython"></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cython"></span>
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147
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184
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<pre style="margin: 0;"> <span id="LC184" 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>
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148
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cython"><span class="c1" style="color: #998; font-style: italic;"># unsigned char[:] (memory view), but this fails with a BufferError</span></span>
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149
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cython"><span class="c1" style="color: #998; font-style: italic;"># when a bytes object is passed in.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="209" style="width: 35px; color: rgba(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">@@ -209,12 +246,19 @@ def fastq_iter(file, sequence_class, Py_ssize_t buffer_size):</td>
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209
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">bytearray</span> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bytearray</span><span class="p">(</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>
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210
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[:]</span> <span class="n" style="color: #333;">buf_view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span></span>
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211
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">char</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;">buf</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">endskip</span></span>
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213
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">str</span> <span class="n" style="color: #333;">name</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">name_encoded</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">bufstart</span><span class="p">,</span> <span class="n" style="color: #333;">bufend</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">record_start</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_start</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">second_header_start</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_length</span><span class="p">,</span> <span class="n" style="color: #333;">qualities_start</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">second_header_length</span><span class="p">,</span> <span class="n" style="color: #333;">name_length</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">str</span> <span class="n" style="color: #333;">sequence</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">str</span> <span class="n" style="color: #333;">qualities</span></span>
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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">last_read_position</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">record_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">bufstart</span><span class="p">,</span> <span class="n" style="color: #333;">bufend</span><span class="p">,</span> <span class="n" style="color: #333;">name_start</span><span class="p">,</span> <span class="n" style="color: #333;">name_end</span><span class="p">,</span> <span class="n" style="color: #333;">name_length</span></span>
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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">sequence_start</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_end</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_length</span></span>
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<td class="new_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">second_header_start</span><span class="p">,</span> <span class="n" style="color: #333;">second_header_end</span><span class="p">,</span> <span class="n" style="color: #333;">second_header_length</span></span>
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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">qualities_start</span><span class="p">,</span> <span class="n" style="color: #333;">qualities_end</span><span class="p">,</span> <span class="n" style="color: #333;">qualities_length</span></span>
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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name_end_ptr</span></span>
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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sequence_end_ptr</span></span>
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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">second_header_end_ptr</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qualities_end_ptr</span></span>
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218
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="n" style="color: #333;">custom_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_class</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">Sequence</span></span>
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219
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">Py_ssize_t</span> <span class="n" style="color: #333;">n_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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220
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="n" style="color: #333;">extra_newline</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="296" style="width: 35px; color: rgba(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">@@ -252,138 +296,182 @@ def fastq_iter(file, sequence_class, Py_ssize_t buffer_size):</td>
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252
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cython"> <span class="n" style="color: #333;">bufstart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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253
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cython"> <span class="n" style="color: #333;">bufend</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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254
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cython"> <span class="n" style="color: #333;">extra_newline</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cython"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">last_read_position</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">record_start</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Incomplete FASTQ records are present.</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extra_newline</span><span class="p">:</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Do not report the linefeed that was added by dnaio but</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># was not present in the original input.</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cython"> <span class="n" style="color: #333;">last_read_position</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cython"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="n" style="color: #333;">record_start</span><span class="p">:</span><span class="n" style="color: #333;">last_read_position</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">count</span><span class="p">(</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>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nf" style="color: #900; font-weight: 600;">FastqFormatError</span><span class="p">(</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cython"> <span class="s" style="color: #d14;">'Premature end of file encountered. The incomplete final record was: '</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cython"> <span class="s" style="color: #d14;">'{!r}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">shorten</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">buf</span><span class="p">[</span><span class="n" style="color: #333;">record_start</span><span class="p">:</span><span class="n" style="color: #333;">last_read_position</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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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cython"> <span class="mi" style="color: #099;">500</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cython"> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">n_records</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lines</span><span class="p">)</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># EOF Reached. Stop iterating.</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span></span>
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257
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cython"></span>
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258
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<td class="new_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Parse all complete FASTQ records in this chunk</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" 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;">0</span></span>
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260
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cython"> <span class="n" style="color: #333;">record_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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261
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cython"> <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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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Parse the name (line 0)</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sa">b</span><span class="s" style="color: #d14;">'@'</span><span class="p">:</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nf" style="color: #900; font-weight: 600;">FastqFormatError</span><span class="p">(</span><span class="s" style="color: #d14;">"Line expected to "</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cython"> <span class="s" style="color: #d14;">"start with '@', but found {!r}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">])),</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cython"> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">n_records</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" 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>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bufend</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="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>
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269
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<pre style="margin: 0;">-<span id="LC269" 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>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bufend</span><span class="p">:</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">### Check for a complete record (i.e 4 newlines are present)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Use libc memchr, this optimizes looking for characters by</span></span>
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># using 64-bit integers. See:</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># https://sourceware.org/git/?p=glibc.git;a=blob_plain;f=string/memchr.c;hb=HEAD</span></span>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># void *memchr(const void *str, int c, size_t n)</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cython"> <span class="n" style="color: #333;">name_end_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #900; font-weight: 600;">memchr</span><span class="p">(</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="p">,</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="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">bufend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">record_start</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name_end_ptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NULL</span><span class="p">:</span></span>
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271
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cython"> <span class="n" style="color: #333;">endskip</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><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 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;">\r</span><span class="s" style="color: #d14;">'</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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273
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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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274
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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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275
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<td class="new_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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276
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<td class="new_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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277
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<td class="new_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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278
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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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279
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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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280
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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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281
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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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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cython"></span>
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283
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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>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cython"></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Parse the sequence (line 1)</span></span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span></span>
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<td class="old_line diff-line-num old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bufend</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="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>
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288
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<pre style="margin: 0;">-<span id="LC288" 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>
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<td class="old_line diff-line-num old" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bufend</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># bufend - sequence_start is always nonnegative:</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># - name_end is at most bufend - 1</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># - thus sequence_start is at most bufend</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cython"> <span class="n" style="color: #333;">name_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name_end_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c_buf</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name_end</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="LC330" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_end_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #900; font-weight: 600;">memchr</span><span class="p">(</span><span class="n" style="color: #333;">c_buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sequence_start</span><span class="p">,</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="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">bufend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sequence_start</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_end_ptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NULL</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_end_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c_buf</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cython"> <span class="n" style="color: #333;">second_header_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_end</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="LC335" class="line" lang="cython"> <span class="n" style="color: #333;">second_header_end_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #900; font-weight: 600;">memchr</span><span class="p">(</span><span class="n" style="color: #333;">c_buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">second_header_start</span><span class="p">,</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="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">bufend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">second_header_start</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">second_header_end_ptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NULL</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cython"> <span class="n" style="color: #333;">endskip</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><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 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;">\r</span><span class="s" style="color: #d14;">'</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cython"> <span class="n" style="color: #333;">sequence</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;">sequence_start</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="LC293" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_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;">sequence_start</span></span>
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<pre style="margin: 0;">-<span id="LC294" 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>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Parse second header (line 2)</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cython"> <span class="n" style="color: #333;">second_header_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bufend</span><span class="p">:</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cython"> <span class="n" style="color: #333;">second_header_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">second_header_end_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c_buf</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cython"> <span class="n" style="color: #333;">qualities_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">second_header_end</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cython"> <span class="n" style="color: #333;">qualities_end_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #900; font-weight: 600;">memchr</span><span class="p">(</span><span class="n" style="color: #333;">c_buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">qualities_start</span><span class="p">,</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="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">bufend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">qualities_start</span><span class="p">))</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qualities_end_ptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NULL</span><span class="p">:</span></span>
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299
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sa">b</span><span class="s" style="color: #d14;">'+'</span><span class="p">:</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cython"> <span class="n" style="color: #333;">qualities_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualities_end_ptr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">c_buf</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cython"></span>
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<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</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="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>
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<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nf" style="color: #900; font-weight: 600;">FastqFormatError</span><span class="p">(</span><span class="s" style="color: #d14;">"Line expected to "</span></span>
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cython"> <span class="s" style="color: #d14;">"start with '@', but found {!r}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">record_start</span><span class="p">])),</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cython"> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">n_records</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">second_header_start</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>
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301
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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nf" style="color: #900; font-weight: 600;">FastqFormatError</span><span class="p">(</span><span class="s" style="color: #d14;">"Line expected to "</span></span>
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302
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<td class="new_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="LC302" class="line" lang="cython"> <span class="s" style="color: #d14;">"start with '+', but found {!r}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">pos</span></span><span class="p">])),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cython"> <span class="s" style="color: #d14;">"start with '+', but found {!r}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">second_header_start</span></span><span class="p">])),</span></span>
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303
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cython"> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">n_records</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" 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 class="c1" style="color: #998; font-style: italic;"># skip over the '+'</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cython"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bufend</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="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>
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<td class="old_line diff-line-num old" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
306
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<pre style="margin: 0;">-<span id="LC306" 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>
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<td class="old_line diff-line-num old" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
307
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<td class="new_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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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bufend</span><span class="p">:</span></span>
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308
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<td class="new_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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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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309
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<td class="new_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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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cython"> <span class="n" style="color: #333;">endskip</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><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 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;">\r</span><span class="s" style="color: #d14;">'</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cython"> <span class="n" style="color: #333;">second_header_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;">second_header_start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">second_header_length</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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312
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<td class="new_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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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cython"> <span class="n" style="color: #333;">second_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cython"></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cython"> <span class="n" style="color: #333;">name_start</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 class="c1" style="color: #998; font-style: italic;"># Skip @</span></span>
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<td class="new_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cython"> <span class="n" style="color: #333;">second_header_start</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span> <span class="c1" style="color: #998; font-style: italic;"># Skip +</span></span>
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<td class="new_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
356
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<pre style="margin: 0;">+<span id="LC356" 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;">name_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">name_start</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sequence_start</span></span>
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<td class="new_line diff-line-num new" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cython"> <span class="n" style="color: #333;">second_header_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">second_header_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">second_header_start</span></span>
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<td class="new_line diff-line-num new" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cython"> <span class="n" style="color: #333;">qualities_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualities_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">qualities_start</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cython"></span>
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<td class="new_line diff-line-num new" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Check for \r\n line-endings and compensate</span></span>
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<td class="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">name_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</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;">\r</span><span class="s" style="color: #d14;">'</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cython"> <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>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">sequence_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</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;">\r</span><span class="s" style="color: #d14;">'</span><span class="p">:</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cython"> <span class="n" style="color: #333;">sequence_length</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">second_header_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</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;">\r</span><span class="s" style="color: #d14;">'</span><span class="p">:</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cython"> <span class="n" style="color: #333;">second_header_length</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">qualities_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</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;">\r</span><span class="s" style="color: #d14;">'</span><span class="p">:</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cython"> <span class="n" style="color: #333;">qualities_length</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cython"></span>
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<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">second_header_length</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># should be 0 when only + is present</span></span>
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314
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">name_length</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">second_header_length</span> <span class="ow" style="font-weight: 600;">or</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">c_buf</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">second_header_start</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left right">name_encoded</span></span><span class="p">,</span> <span class="n" style="color: #333;">second_header_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">c_buf</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">second_header_start</span><span class="p">,</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">c_buf</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">name_start</span></span><span class="p">,</span> <span class="n" style="color: #333;">second_header_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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317
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nf" style="color: #900; font-weight: 600;">FastqFormatError</span><span class="p">(</span></span>
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318
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cython"> <span class="s" style="color: #d14;">"Sequence descriptions don't match ('{}' != '{}').</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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319
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cython"> <span class="s" style="color: #d14;">"The second sequence description must be either "</span></span>
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320
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<td class="new_line diff-line-num" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cython"> <span class="s" style="color: #d14;">"empty or equal to the first description."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">name_encoded</span></span><span class="p"><span class="idiff">[</span>:</span><span class="n" style="color: #333;">name_<span class="idiff">l</span>en<span class="idiff right">gth</span></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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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cython"> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">second_header_start</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">:</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">endskip</span></span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">c_buf</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">name_start</span></span><span class="p">:</span><span class="n" style="color: #333;">name_en<span class="idiff right">d</span></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="LC380" class="line" lang="cython"> <span class="n" style="color: #333;">c_buf</span><span class="p">[</span><span class="n" style="color: #333;">second_header_start</span><span class="p"><span class="idiff left">:</span></span><span class="n" style="color: #333;"><span class="idiff right">second_header_end</span></span><span class="p">]</span></span>
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cython"> <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 class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">n_records</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cython"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">second_header</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># Parse qualities (line</span> 3)</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cython"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">qualities_start</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pos</span></span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cython"> <span class="k" style="font-weight: 600;"><span class="idiff left">while</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bufend</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">c_buf</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="sa"><span class="idiff">b</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">:</span></span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cython"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="cython"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bufend</span></span><span class="p"><span class="idiff right">:</span></span></span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cython"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">break</span></span></span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">endskip</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">c_buf</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="sa"><span class="idiff">b</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\r</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">qualities</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">c_buf</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">qualities_start</span></span><span class="p"><span class="idiff">:</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">endskip</span></span><span class="p"><span class="idiff">].</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">decode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'latin-1'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="cython"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">endskip</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualities_start</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence_length</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC336" class="line" lang="cython"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">raise</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">FastqFormatError</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Length of sequence and "</span></span></span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cython"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span>qualities <span class="idiff">differ"</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="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">n_records</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">)</span></span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cython"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cython"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualities_length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence_length</span></span><span class="p"><span class="idiff right">:</span></span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nf" style="color: #900; font-weight: 600;">FastqFormatError</span><span class="p">(</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cython"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"Length of sequence and qualities differ"</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="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">n_records</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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386
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">### Copy record into python variables</span></span></span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># PyUnicode_DecodeLatin1 is 50% faster than PyUnicode_DecodeASCII.</span></span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># This is because PyUnicode_DecodeLatin1 is an alias for</span></span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># _PyUnicode_FromUCS1. Which directly copies the bytes into a</span></span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># string object after some checks. With PyUnicode_DecodeASCII,</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># there is an extra check whether characters exceed 128.</span></span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">name</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">PyUnicode_DecodeLatin1</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">c_buf</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name_start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name_length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'strict'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">sequence</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">PyUnicode_DecodeLatin1</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">c_buf</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence_start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sequence_length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'strict'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cython"> <span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">PyUnicode_DecodeLatin1</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">c_buf</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualities_start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualities_length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'strict'</span></span><span class="p">)</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cython"></span>
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339
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n_records</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cython"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">second_header</span> <span class="c1" style="color: #998; font-style: italic;"># first yielded value is special</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cython"> <span class="k" style="font-weight: 600;">yield</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">bool</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">second_header<span class="idiff">_length</span></span><span class="p"><span class="idiff right">)</span></span> <span class="c1" style="color: #998; font-style: italic;"># first yielded value is special</span></span>
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341
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">custom_class</span><span class="p">:</span></span>
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342
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cython"> <span class="k" style="font-weight: 600;">yield</span> <span class="nf" style="color: #900; font-weight: 600;">sequence_class</span><span class="p">(</span><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>
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343
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<td class="new_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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344
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<td class="new_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cython"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">Sequence</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">__new__</span><span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <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>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cython"></span>
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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">### Advance record to next position</span></span>
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345
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cython"> <span class="n" style="color: #333;">n_records</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cython"> <span class="n" style="color: #333;">record_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span></span>
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347
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bufend</span><span class="p">:</span></span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="cython"> <span class="k" style="font-weight: 600;">break</span></span>
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349
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bufend</span><span class="p">:</span></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record_start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">bufend</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;">buf</span><span class="p">):</span></span>
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351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># buffer too small, double it</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="cython"> <span class="n" style="color: #333;">buffer_size</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">2</span></span>
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353
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cython"> <span class="n" style="color: #333;">prev_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span></span>
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354
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cython"> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bytearray</span><span class="p">(</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cython"> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="n" style="color: #333;">bufend</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prev_buf</span></span>
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356
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="cython"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">prev_buf</span></span>
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357
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cython"> <span class="n" style="color: #333;">bufstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bufend</span></span>
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<td class="old_line diff-line-num old" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
358
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="cython"> <span class="n" style="color: #333;">buf_view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span></span>
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359
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="cython"> <span class="n" style="color: #333;">c_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span></span>
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360
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
361
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="cython"> <span class="n" style="color: #333;">bufstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bufend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">record_start</span></span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="cython"> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="n" style="color: #333;">bufstart</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="n" style="color: #333;">record_start</span><span class="p">:</span><span class="n" style="color: #333;">bufend</span><span class="p">]</span></span>
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363
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">record_start</span><span class="p">:</span></span>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extra_newline</span><span class="p">:</span></span>
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365
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC365" 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>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cython"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="n" style="color: #333;">record_start</span><span class="p">:</span><span class="n" style="color: #333;">pos</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">count</span><span class="p">(</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>
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367
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nf" style="color: #900; font-weight: 600;">FastqFormatError</span><span class="p">(</span></span>
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368
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="cython"> <span class="s" style="color: #d14;">'Premature end of file encountered. The incomplete final record was: '</span></span>
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369
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<td class="new_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">
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cython"> <span class="s" style="color: #d14;">'{!r}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">shorten</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">buf</span><span class="p">[</span><span class="n" style="color: #333;">record_start</span><span class="p">:</span><span class="n" style="color: #333;">pos</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 class="mi" style="color: #099;">500</span><span class="p">)),</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cython"> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">n_records</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lines</span><span class="p">)</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cython"> <span class="n" style="color: #333;">record_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualities_end</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># bufend reached</span></span>
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cython"> <span class="n" style="color: #333;">last_read_position</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bufend</span></span>
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record_start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">bufend</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;">buf</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># buffer too small, double it</span></span>
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<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cython"> <span class="n" style="color: #333;">buffer_size</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cython"> <span class="n" style="color: #333;">prev_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span></span>
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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cython"> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bytearray</span><span class="p">(</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cython"> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="n" style="color: #333;">bufend</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prev_buf</span></span>
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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cython"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">prev_buf</span></span>
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<td class="new_line diff-line-num new" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cython"> <span class="n" style="color: #333;">bufstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bufend</span></span>
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<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cython"> <span class="n" style="color: #333;">buf_view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cython"> <span class="n" style="color: #333;">c_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cython"> <span class="n" style="color: #333;">bufstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bufend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">record_start</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cython"> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="n" style="color: #333;">bufstart</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="n" style="color: #333;">record_start</span><span class="p">:</span><span class="n" style="color: #333;">bufend</span><span class="p">]</span></span>
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371
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cython"></span>
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372
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="cython"></span>
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373
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cython"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">record_names_match</span><span class="p">(</span><span class="n" style="color: #333;">header1</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">header2</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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374
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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375
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cython"><span class="s" style="color: #d14;"> Check whether the sequence record ids id1 and id2 are compatible, ignoring a</span></span>
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376
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cython"><span class="s" style="color: #d14;"> suffix of '1', '2' or '3'. This exception allows to check some old</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cython"><span class="s" style="color: #d14;"> paired-end reads that have <span class="idiff left right">name</span>s ending in '/1' and '/2'. Also, the</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cython"><span class="s" style="color: #d14;"> paired-end reads that have <span class="idiff left right">ID</span>s ending in '/1' and '/2'. Also, the</span></span>
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378
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cython"><span class="s" style="color: #d14;"> fastq-dump tool (used for converting SRA files to FASTQ) appends '.1', '.2'</span></span>
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379
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cython"><span class="s" style="color: #d14;"> and sometimes '.3' to paired-end reads if option -I is used.</span></span>
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380
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431
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span><span class="p">:</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">str</span> <span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cython"></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cython"> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cython"> <span class="n" style="color: #333;">name2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header2</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name1</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="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">'123'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name2</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="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">'123'</span><span class="p">:</span></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="cython"> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name1</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>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cython"> <span class="n" style="color: #333;">name2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name2</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>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">PyUnicode_KIND</span><span class="p">(</span><span class="n" style="color: #333;">header1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">PyUnicode_1BYTE_KIND</span> <span class="ow" style="font-weight: 600;">or</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">PyUnicode_KIND</span><span class="p">(</span><span class="n" style="color: #333;">header2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">PyUnicode_1BYTE_KIND</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cython"> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Fall back to slower code path.</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cython"> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="n" style="color: #333;">maxsplit</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;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cython"> <span class="n" style="color: #333;">name2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header2</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="n" style="color: #333;">maxsplit</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;">0</span><span class="p">]</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name1</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="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">'123'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name2</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="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">'123'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name1</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="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name2</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>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name2</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Do not call .encode functions but use the unicode pointer inside the</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># python object directly, provided it is in 1-byte encoding, so we can</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># find the spaces and tabs easily.</span></span>
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<pre style="margin: 0;">+<span id="LC445" 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;">header1_chars</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #900; font-weight: 600;">PyUnicode_1BYTE_DATA</span><span class="p">(</span><span class="n" style="color: #333;">header1</span><span class="p">)</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" 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;">header2_chars</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*></span><span class="nf" style="color: #900; font-weight: 600;">PyUnicode_1BYTE_DATA</span><span class="p">(</span><span class="n" style="color: #333;">header2</span><span class="p">)</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">header1_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="nf" style="color: #900; font-weight: 600;">PyUnicode_GET_LENGTH</span><span class="p">(</span><span class="n" style="color: #333;">header1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">record_ids_match</span><span class="p">(</span><span class="n" style="color: #333;">header1_chars</span><span class="p">,</span> <span class="n" style="color: #333;">header2_chars</span><span class="p">,</span> <span class="n" style="color: #333;">header1_length</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="nf" style="color: #900; font-weight: 600;">record_ids_match</span><span class="p">(</span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header1</span><span class="p">,</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">header1_length</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cython"><span class="s" style="color: #d14;"> Check whether the ASCII-encoded IDs match. Only header1_length is needed.</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Only the read ID is of interest.</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Find the first tab or space, if not present, strcspn will return the</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># position of the terminating NULL byte. (I.e. the length).</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Header1 is not searched because we can reuse the end of ID position of</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># header2 as header1's ID should end at the same position.</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">id2_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">strcspn</span><span class="p">(</span><span class="n" style="color: #333;">header2</span><span class="p">,</span> <span class="sa">b</span><span class="s" style="color: #d14;">' </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header1_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">id2_length</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header1</span><span class="p">[</span><span class="n" style="color: #333;">id2_length</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">end</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;">\000</span><span class="s" style="color: #d14;">'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sa">b</span><span class="s" style="color: #d14;">' '</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">end</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;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Check if the IDs end with 1, 2 or 3. This is the read pair number</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># which should not be included in the comparison.</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="n" style="color: #333;">id1endswithnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">b</span><span class="s" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">header1</span><span class="p">[</span><span class="n" style="color: #333;">id2_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="sa">b</span><span class="s" style="color: #d14;">'3'</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="n" style="color: #333;">id2endswithnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">b</span><span class="s" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">header2</span><span class="p">[</span><span class="n" style="color: #333;">id2_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="sa">b</span><span class="s" style="color: #d14;">'3'</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">id1endswithnumber</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">id2endswithnumber</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cython"> <span class="n" style="color: #333;">id2_length</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="LC475" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Compare the strings up to the ID end position.</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">memcmp</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">void</span> <span class="o" style="font-weight: 600;">*></span><span class="n" style="color: #333;">header1</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">void</span> <span class="o" style="font-weight: 600;">*></span><span class="n" style="color: #333;">header2</span><span class="p">,</span> <span class="n" style="color: #333;">id2_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span></pre>
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<li id="b31d13e8151f786e577da1e989935f7ba967c4e8">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#b31d13e8151f786e577da1e989935f7ba967c4e8"><strong>src/dnaio/chunks.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">@@ -16,9 +16,15 @@ def _fasta_head(buf: bytes, end: Optional[int] = None) -> int:</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span><span class="p">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</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="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <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>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">buf</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="o" style="font-weight: 600;">==</span> <span class="sa">b</span><span class="s" style="color: #d14;">'>'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">buf</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="o" style="font-weight: 600;">==</span> <span class="sa">b</span><span class="s" style="color: #d14;">'>'</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">buf</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">:</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="sa"><span class="idiff">b</span></span><span class="s" style="color: #d14;"><span class="idiff right">'#'</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC21" 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 class="s" style="color: #d14;">'File does not start with ">"'</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="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC24" 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>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"FASTA file expected to start with '>', but found </span><span class="si" style="color: #d14;">{</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">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="LC27" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_fastq_head</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bytes</span><span class="p">,</span> <span class="n" style="color: #333;">end</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 class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">int</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">@@ -52,15 +58,19 @@ def read_chunks(f: RawIOBase, buffer_size: int = 4 * 1024**2) -> Iterator[memory</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read one byte to determine file format.</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If there is a comment char, we assume FASTA!</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">readinto</span><span class="p">(</span><span class="nb" style="color: #0086b3;">memoryview</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">buf</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="o" style="font-weight: 600;">==</span> <span class="sa">b</span><span class="s" style="color: #d14;">'@'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_fastq_head</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">buf</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="o" style="font-weight: 600;">==</span> <span class="sa">b</span><span class="s" style="color: #d14;">'#'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">buf</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="o" style="font-weight: 600;">==</span> <span class="sa">b</span><span class="s" style="color: #d14;">'>'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_fasta_head</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Empty file</span></span>
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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>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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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;">buf</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="o" style="font-weight: 600;">==</span> <span class="sa">b</span><span class="s" style="color: #d14;">'@'</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;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_fastq_head</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">buf</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="o" style="font-weight: 600;">==</span> <span class="sa">b</span><span class="s" style="color: #d14;">'#'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">buf</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="o" style="font-weight: 600;">==</span> <span class="sa">b</span><span class="s" style="color: #d14;">'>'</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;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_fasta_head</span></span>
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<pre style="margin: 0;"> <span id="LC69" 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="LC63" 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 class="s" style="color: #d14;">'Input file format unknown'</span><span class="p">)</span></span>
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<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;">UnknownFileFormat</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"Cannnot determine input file format: First character expected to be '>' or '@', "</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="sa">f</span><span class="s" style="color: #d14;">"but found </span><span class="si" style="color: #d14;">{</span><span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Layout of buf</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<li id="a66e9807f4b39aaa61baab58ad1a281bd6691999">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#a66e9807f4b39aaa61baab58ad1a281bd6691999"><strong>src/dnaio/pairedend.py</strong></a>
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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;">itertools</span></span>
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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;">contextlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ExitStack</span></span>
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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;">os</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PathLike</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">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>
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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">@@ -47,26 +48,24 @@ class TwoFilePairedEndReader(PairedEndReader):</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> Iterate over the paired reads. Each item is a pair of Sequence objects.</span></span>
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<pre style="margin: 0;"> <span id="LC50" 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>
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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>
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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>
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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>
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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>
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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>
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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>
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<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>
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<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>
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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>
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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>
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<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>
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<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>
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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>
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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>
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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>
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<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>
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<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>
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<pre style="margin: 0;">+<span id="LC51" 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="LC52" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># when one of the iterators is exhausted. zip in python 3.10 has a</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 'strict' keyword that can be used to prevent this and throw an error,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># but it will take a long time for 3.10 or higher to be available on</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># everyone's machine.</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Instead use zip_longest from itertools. This yields None if one of</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the iterators is exhausted. Checking for None identity is fast.</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># So we can quickly check if the iterator is still yielding.</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This is faster than implementing a while loop with next calls,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># which requires expensive function lookups.</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="p">.</span><span class="n" style="color: #333;">zip_longest</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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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r1</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">(</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">"Reads are improperly paired. There are more reads in "</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">"file 2 than in file 1."</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;">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="LC67" 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>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="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="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">"Reads are improperly paired. There are more reads in "</span></span>
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72
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="s" style="color: #d14;">"file 1 than in file 2."</span><span class="p">,</span></span>
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<li id="79bba35b6cf4519cc3ab15da71893164d46ad480">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#79bba35b6cf4519cc3ab15da71893164d46ad480"><strong>src/dnaio/readers.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">@@ -121,7 +121,7 @@ class FastqReader(BinaryFileReader, SingleEndReader):</td>
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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>
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122
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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>
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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>
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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;">1<span class="idiff left">048576</span></span><span class="p"><span class="idiff right">,</span></span></span>
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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;">1<span class="idiff left">28</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1024</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># Buffer size used by cat, pigz etc.</span></span></span>
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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>
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<pre style="margin: 0;"> <span id="LC126" 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>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#09b1291e3cfc7a40be592455cb1acaacfa12b950"><strong>src/dnaio/singleend.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">@@ -112,10 +112,11 @@ def _detect_format_from_content(file: BinaryIO) -> Optional[str]:</td>
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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>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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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>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">original_position</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;">tell</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">first_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<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>
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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>
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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="n" style="color: #333;">original_position</span><span class="p">)</span></span>
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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>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># We cannot always use peek() because BytesIO objects do not suppert it</span></span>
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<pre style="margin: 0;"> <span id="LC120" 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="LC121" 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="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;">"fastq"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#ac9c6701e83ec81d3f6fff83e5237d3f8bcb18c2"><strong>tests/test_chunks.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">@@ -2,7 +2,33 @@ from pytest import raises</td>
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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;">io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BytesIO</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio._core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">paired_fastq_heads</span></span>
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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;">dnaio.chunks</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_fastq_head</span><span class="p">,</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="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio.chunks</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_fastq_head</span><span class="p">,</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">,</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="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fasta_head</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">''</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>6'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>6</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>6</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">8'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>6</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">8</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>6</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">8</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">0'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>6</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">8</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>6</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">8</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">12</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fasta_head_with_comment</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'#'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</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="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</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="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</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;">>3'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</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;">>3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</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;">>3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">5'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</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;">>3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">5</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">_fasta_head</span><span class="p">(</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;">>3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">5</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">>'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_paired_fastq_heads</span><span class="p">():</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#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">@@ -239,7 +239,7 @@ class TestFastqReader:</td>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">fq</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_second_header_not_equal</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="LC242" class="line" lang="python"> <span class="n" style="color: #333;">fastq</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;">+xy</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="LC242" class="line" lang="python"> <span class="n" style="color: #333;">fastq</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;">+xy</span><span class="se" style="color: #d14;">\<span class="idiff left">n</span></span><span class="s" style="color: #d14;"><span class="idiff">XXX</span></span><span class="se" style="color: #d14;"><span class="idiff right">\</span>n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC243" 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;">FastqFormatError</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="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">FastqReader</span><span class="p">(</span><span class="n" style="color: #333;">fastq</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fq</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">fq</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># pragma: no cover</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">@@ -482,6 +482,11 @@ class TestPairedSequenceReader:</td>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'abc def'</span><span class="p">,</span> <span class="s" style="color: #d14;">'abc ghi'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'abc'</span><span class="p">,</span> <span class="s" style="color: #d14;">'abc ghi'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'abc'</span><span class="p">,</span> <span class="s" style="color: #d14;">'xyz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'abc</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">def'</span><span class="p">,</span> <span class="s" style="color: #d14;">'abc'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'abc</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">def'</span><span class="p">,</span> <span class="s" style="color: #d14;">'abc</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ghi'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'abc somecomment</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">anothercomment'</span><span class="p">,</span> <span class="s" style="color: #d14;">'abc andanothercomment</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bla'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'abc</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">comments comments'</span><span class="p">,</span> <span class="s" style="color: #d14;">'abc</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">others others'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'abc</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">def'</span><span class="p">,</span> <span class="s" style="color: #d14;">'abc def'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_record_names_match_with_ignored_trailing_12</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="LC492" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record_names_match</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">@@ -521,6 +526,15 @@ class TestPairedSequenceReader:</td>
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<pre style="margin: 0;"> <span id="LC526" 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>
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<pre style="margin: 0;"> <span id="LC527" 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>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_empty_sequences_do_not_stop_iteration</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="LC530" 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;">@r2_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;">@r3_2</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="LC531" 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_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;">@r2_2</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">@r3_2</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="LC532" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Second sequence for s2 is empty but valid. Should not lead to a stop of iteration.</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">TwoFilePairedEndReader</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="LC534" class="line" lang="python"> <span class="n" style="color: #333;">seqs</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>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC538" 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="LC539" 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>
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<pre style="margin: 0;"> <span id="LC540" 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>
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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">@@ -531,18 +545,21 @@ class TestPairedSequenceReader:</td>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">'path'</span><span class="p">,</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'tests/data/</span>simple.fastq'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'tests/data/</span>dos.fastq'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'tests/data/</span>simple.fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'tests/data/</span>with_comment.fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'tests'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'</span>simple.fastq'</span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'tests'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'</span>dos.fastq'</span><span class="p"><span class="idiff right">)</span>,</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'tests'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'</span>simple.fasta'</span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'tests'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'data'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'</span>with_comment.fasta'</span><span class="p"><span class="idiff right">)</span>,</span></span>
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_read_stdin</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get number of records in the input file</span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Use 'cat' to simulate that no file name is available for stdin of the subprocess</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span><span class="s" style="color: #d14;">'cat'</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">cat</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Use piping from a separate subprocess to force the input file name to be unavailable</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"type"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">platform</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"win32"</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"cat"</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">platform</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"win32"</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">cat</span><span class="p">:</span></span>
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span></span>
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547
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">'tests/read_from_stdin.py'</span><span class="p">],</span> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cat</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"> <span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">py</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/compare/ec0066b8b6e9334440e0d82ed774937d4514f646...0f3b72fc4ed67d190b1f3eea27f380deee9aaec7#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c"><strong>tox.ini</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="ini"><span class="nn" style="color: #555;">[tox]</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="ini"><span class="py">envlist</span> <span class="p">=</span> <span class="s" style="color: #d14;">flake8,mypy,py36,py37,py38,py39</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="ini"><span class="py"><span class="idiff left">requires</span></span><span class="idiff"> </span><span class="p"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">Cython>=0.29.13</span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="ini"><span class="py">envlist</span> <span class="p">=</span> <span class="s" style="color: #d14;">flake8,mypy,py36,py37,py38,py39<span class="idiff left right">,py310</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="ini"><span class="py"><span class="idiff left">isolated_build</span></span><span class="idiff"> </span><span class="p"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">True</span></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="ini"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv]</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="ini"><span class="py">deps</span> <span class="p">=</span></span>
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