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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-nanomath">Debian Med / python-nanomath</a>
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<h4>
Commits:
</h4>
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<strong><a href="https://salsa.debian.org/med-team/python-nanomath/-/commit/461e5d26467062fbb1c665e294418b4ec57eea30">461e5d26</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-05-16T18:56:01+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.1+ds</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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<li class="file-stats">
<a href="#c721ed908bd00486c8fdcff084a92306d03e39eb">
nanomath.egg-info/PKG-INFO
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<li class="file-stats">
<a href="#bd8fd9949a7d37dd1ed7e503c3f6e15c777068ab">
nanomath/nanomath.py
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<li class="file-stats">
<a href="#d53a95c2a92a11bea71b033634233d5fa3e77146">
nanomath/version.py
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<h4>Changes:</h4>
<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/python-nanomath/-/commit/461e5d26467062fbb1c665e294418b4ec57eea30#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.2</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: nanomath</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.2.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.2.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A few simple math function for other Oxford Nanopore processing scripts</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/wdecoster/nanomath</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Wouter De Coster</span>
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<a href="https://salsa.debian.org/med-team/python-nanomath/-/commit/461e5d26467062fbb1c665e294418b4ec57eea30#c721ed908bd00486c8fdcff084a92306d03e39eb"><strong>nanomath.egg-info/PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.2</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: nanomath</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.2.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.2.<span class="idiff left right">1</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A few simple math function for other Oxford Nanopore processing scripts</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/wdecoster/nanomath</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Wouter De Coster</span>
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<li id="bd8fd9949a7d37dd1ed7e503c3f6e15c777068ab">
<a href="https://salsa.debian.org/med-team/python-nanomath/-/commit/461e5d26467062fbb1c665e294418b4ec57eea30#bd8fd9949a7d37dd1ed7e503c3f6e15c777068ab"><strong>nanomath/nanomath.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,6 +53,11 @@ class Stats(object):</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">col</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"quals"</span><span class="p">,</span></span>
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths"</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reads_above_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">reads_above_qual</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_qualgroups</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC56" 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="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_top5_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_top_5</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</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;">col</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"lengths"</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;">values</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">],</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">fill</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'quals'</span><span class="p">)</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">long_features_as_string</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="python"> <span class="s" style="color: #d14;">"""formatting long features to a string to print for legacy stats output"""</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">@@ -95,12 +100,16 @@ class Stats(object):</td>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">unwind_long_features_top5</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">"""for tsv stats output"""</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">feature</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">:</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">entry</span><span class="p">,</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)):</span></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</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="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">label</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{} ({})'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">ndigits</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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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">ndigits</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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101
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">unwind_long_features_above_qual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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103
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="s" style="color: #d14;">"""for tsv stats output"""</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">feature</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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104
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">entry</span><span class="p">,</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">],</span></span>
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105
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'>Q{}:'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_qualgroups</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;">numberAboveQ</span><span class="p">,</span> <span class="n" style="color: #333;">megAboveQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entry</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">@@ -148,13 +157,20 @@ def ave_qual(quals, qround=False, tab=errs_tab(128)):</td>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_top_5</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_top_5</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fill</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"readIDs"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">values</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"readIDs"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">ascending</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span> \</span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">head</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">)[</span><span class="n" style="color: #333;">values</span><span class="p">]</span> \</span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</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="LC157" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">itertuples</span><span class="p">(</span><span class="n" style="color: #333;">index</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;">name</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="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fill</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">ascending</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span> \</span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">head</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">)[</span><span class="n" style="color: #333;">values</span><span class="p">]</span> \</span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">fill</span><span class="o" style="font-weight: 600;">=</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="mi" style="color: #099;">5</span><span class="p">)</span> \</span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</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="LC168" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">itertuples</span><span class="p">(</span><span class="n" style="color: #333;">index</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;">name</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="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">ascending</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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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">head</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">)[</span><span class="n" style="color: #333;">values</span><span class="p">]</span> \</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</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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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">itertuples</span><span class="p">(</span><span class="n" style="color: #333;">index</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;">name</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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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"></span>
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159
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"></span>
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160
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reads_above_qual</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.2.<span class="idiff left right">0</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.2.<span class="idiff left right">1</span>"</span></span></pre>
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