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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-dnaio">Debian Med / python-dnaio</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/850ea9ad1ba0e6e63c8315deec863b4288833f17">850ea9ad</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-04-30T22:47:56+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.4.2</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#38e7f48281a2602f08cb832d9472eb2330e11e51">
src/dnaio/__init__.py
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<li class="file-stats">
<a href="#72ff21bf4040f97f9c5919d676e807b4117d01b7">
src/dnaio/_core.pyx
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<li class="file-stats">
<a href="#2c796bdd402f95103c9d6524cf0927843f28bec8">
src/dnaio/writers.py
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<li class="file-stats">
<a href="#307d17476eda4102236d69ec93ead958067e02d6">
tests/test_internal.py
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<h4>Changes:</h4>
<li id="38e7f48281a2602f08cb832d9472eb2330e11e51">
<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/850ea9ad1ba0e6e63c8315deec863b4288833f17#38e7f48281a2602f08cb832d9472eb2330e11e51"><strong>src/dnaio/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,7 +28,7 @@ import pathlib</td>
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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 class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">record_names_match</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_record_names_match</span></span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.readers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span></span>
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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;">.writers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">,</span> <span class="n" style="color: #333;">FileFormatError</span><span class="p">,</span> <span class="n" style="color: #333;">FastaFormatError</span><span class="p">,</span> <span class="n" style="color: #333;">FastqFormatError</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(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="212" style="width: 35px; color: rgba(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">@@ -212,21 +212,6 @@ def _detect_format_from_content(file):</td>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">formats</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">first_char</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_sequence_names_match</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;"> Check whether the sequence records r1 and r2 have identical names, ignoring a</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"><span class="s" style="color: #d14;"> suffix of '1' or '2'. Some old paired-end reads have names that end in '/1'</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"><span class="s" style="color: #d14;"> and '/2'. Also, the fastq-dump tool (used for converting SRA files to FASTQ)</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"><span class="s" style="color: #d14;"> appends a .1 and .2 to paired-end reads if option -I is used.</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">None</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>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">name2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">None</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>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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;">'12'</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;">'12'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <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="LC226" class="line" lang="python"> <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="LC227" class="line" lang="python"> <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="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedSequenceReader</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;"> Read paired-end reads from two files.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(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="253" style="width: 35px; color: rgba(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">@@ -268,7 +253,7 @@ class PairedSequenceReader:</td>
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<pre style="margin: 0;"> <span id="LC253" 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="LC254" 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="LC255" class="line" lang="python"> <span class="s" style="color: #d14;">"file 1 than in file 2."</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">_<span class="idiff left">sequence_names_match</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">r2</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">_<span class="idiff left">record_names_match</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">r2</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">name</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC257" 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="LC258" class="line" lang="python"> <span class="s" style="color: #d14;">"Reads are improperly paired. Read name '{}' "</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="s" style="color: #d14;">"in file 1 does not match '{}' in file 2."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="303" style="width: 35px; color: rgba(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="288" style="width: 35px; color: rgba(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">@@ -303,7 +288,7 @@ class InterleavedSequenceReader:</td>
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<pre style="margin: 0;"> <span id="LC288" 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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304
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"> <span class="s" style="color: #d14;">"Interleaved input file incomplete: Last record "</span></span>
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305
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="s" style="color: #d14;">"{!r} has no partner."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">_<span class="idiff left">sequence_names_match</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">r2</span></span><span class="p">):</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">_<span class="idiff left">record_names_match</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">r2</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">name</span></span><span class="p">):</span></span>
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307
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292
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<pre style="margin: 0;"> <span id="LC292" 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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308
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="s" style="color: #d14;">"Reads are improperly paired. Name {!r} "</span></span>
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309
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="s" style="color: #d14;">"(first) does not match {!r} (second)."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/850ea9ad1ba0e6e63c8315deec863b4288833f17#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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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;">libc.string</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">strncmp</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;">libc.string</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">strncmp</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">memcmp</span></span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cython"><span class="kn" style="font-weight: 600;">cimport</span> <span class="nn" style="color: #555;">cython</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cython"></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;">.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastqFormatError</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,6 +62,16 @@ cdef class Sequence:</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__reduce__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qualities</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fastq_bytes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cython"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'@'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="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="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">'</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cython"> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="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>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cython"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cython"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'@'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">+'</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cython"> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="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>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC76" 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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<pre style="margin: 0;"> <span id="LC77" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="282" style="width: 35px; color: rgba(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="292" style="width: 35px; color: rgba(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">@@ -282,3 +292,21 @@ def fastq_iter(file, sequence_class, Py_ssize_t buffer_size):</td>
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282
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292
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<pre style="margin: 0;"> <span id="LC292" 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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283
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293
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<pre style="margin: 0;"> <span id="LC293" 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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284
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294
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<pre style="margin: 0;"> <span id="LC294" 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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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cython"></span>
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296
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297
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<pre style="margin: 0;">+<span id="LC297" 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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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC299" 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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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cython"><span class="s" style="color: #d14;"> suffix of '1' or '2'. Some old paired-end reads have names that end in '/1'</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cython"><span class="s" style="color: #d14;"> and '/2'. Also, the fastq-dump tool (used for converting SRA files to FASTQ)</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cython"><span class="s" style="color: #d14;"> appends a .1 and .2 to paired-end reads if option -I is used.</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># TODO optimize this a bit more</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;">cdef</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="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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307
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<pre style="margin: 0;">+<span id="LC307" 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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308
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<pre style="margin: 0;">+<span id="LC308" 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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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</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;">'12'</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;">'12'</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;">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="LC311" 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="LC312" 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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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/850ea9ad1ba0e6e63c8315deec863b4288833f17#2c796bdd402f95103c9d6524cf0927843f28bec8"><strong>src/dnaio/writers.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">@@ -81,17 +81,21 @@ class FastqWriter(FileWriter):</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">two_headers</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xopen</span><span class="p">,</span> <span class="n" style="color: #333;">_close_file</span><span class="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="LC82" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">opener</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">opener</span><span class="p">,</span> <span class="n" style="color: #333;">_close_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_close_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_two_headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">two_headers</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write_two_headers</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_two_headers</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">_</span>write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"><span class="s" style="color: #d14;"> Write a Sequence record to the FASTQ file.</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> The record object must have attributes .name, .sequence and .qualities.</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">name2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_two_headers</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'@'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">+'</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">name2</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="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>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">fastq_bytes</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_write_two_headers</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;"> Write a Sequence record to the FASTQ file, repeating the header</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;"> in the third line after the "+" .</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">fastq_bytes_two_headers</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeseq</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="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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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"@{0:s}</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">{1:s}</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">+</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">{2:s}</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<a href="https://salsa.debian.org/med-team/python-dnaio/-/commit/850ea9ad1ba0e6e63c8315deec863b4288833f17#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">@@ -14,7 +14,7 @@ from dnaio import (</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">FastaReader</span><span class="p">,</span> <span class="n" style="color: #333;">FastqReader</span><span class="p">,</span> <span class="n" style="color: #333;">InterleavedSequenceReader</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;">FastaWriter</span><span class="p">,</span> <span class="n" style="color: #333;">FastqWriter</span><span class="p">,</span> <span class="n" style="color: #333;">InterleavedSequenceWriter</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">PairedSequenceReader</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_<span class="idiff left right">sequence</span>_names_match</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_<span class="idiff left right">record</span>_names_match</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># files tests/data/simple.fast{q,a}</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">@@ -462,12 +462,8 @@ class TestPairedSequenceReader:</td>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"r1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"HHH"</span><span class="p">),</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"r2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GTT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"858"</span><span class="p">)),</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python"> <span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">psr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sequence_names_match</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="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">match</span><span class="p">(</span><span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="python"> <span class="n" style="color: #333;">seq1</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;">name1</span><span class="p">,</span> <span class="s" style="color: #d14;">'ACGT'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">seq2</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;">name2</span><span class="p">,</span> <span class="s" style="color: #d14;">'AACC'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_sequence_names_match</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC465" 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</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="LC466" 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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<pre style="margin: 0;"> <span id="LC467" 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'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC468" 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/1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'abc/2'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC469" 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.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'abc.2'</span><span class="p">)</span></span>
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