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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<title>OBITools V4 - 4&nbsp; Annexes</title>
<title>OBITools V4 - 5&nbsp; Annexes</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
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<header id="quarto-header" class="headroom fixed-top">
<nav class="quarto-secondary-nav" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<div class="container-fluid d-flex justify-content-between">
<h1 class="quarto-secondary-nav-title"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Annexes</span></h1>
<h1 class="quarto-secondary-nav-title"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Annexes</span></h1>
<button type="button" class="quarto-btn-toggle btn" aria-label="Show secondary navigation">
<i class="bi bi-chevron-right"></i>
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</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./commands.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">The <em>OBITools V4</em> commands</span></a>
<a href="./tutorial.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">OBITools V4 Tutorial</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./library.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">The GO <em>OBITools</em> library</span></a>
<a href="./commands.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">The <em>OBITools V4</em> commands</span></a>
</div>
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<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./annexes.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Annexes</span></a>
<a href="./library.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">The GO <em>OBITools</em> library</span></a>
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<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./annexes.html" class="sidebar-item-text sidebar-link active"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Annexes</span></a>
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<h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#sequence-attributes" id="toc-sequence-attributes" class="nav-link active" data-scroll-target="#sequence-attributes"><span class="toc-section-number">4.0.1</span> Sequence attributes</a></li>
<li><a href="#sequence-attributes" id="toc-sequence-attributes" class="nav-link active" data-scroll-target="#sequence-attributes"><span class="toc-section-number">5.0.1</span> Sequence attributes</a></li>
</ul>
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<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title d-none d-lg-block"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Annexes</span></h1>
<h1 class="title d-none d-lg-block"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Annexes</span></h1>
</div>
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</header>
<section id="sequence-attributes" class="level3" data-number="4.0.1">
<h3 data-number="4.0.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">4.0.1</span> Sequence attributes</h3>
<section id="reserved-sequence-attributes" class="level4" data-number="4.0.1.1">
<h4 data-number="4.0.1.1" class="anchored" data-anchor-id="reserved-sequence-attributes"><span class="header-section-number">4.0.1.1</span> Reserved sequence attributes</h4>
<section id="ali_dir" class="level5" data-number="4.0.1.1.1">
<h5 data-number="4.0.1.1.1" class="anchored" data-anchor-id="ali_dir"><span class="header-section-number">4.0.1.1.1</span> <code>ali_dir</code></h5>
<section id="type-string" class="level6" data-number="4.0.1.1.1.1">
<h6 data-number="4.0.1.1.1.1" class="anchored" data-anchor-id="type-string"><span class="header-section-number">4.0.1.1.1.1</span> Type : <code>string</code></h6>
<section id="sequence-attributes" class="level3" data-number="5.0.1">
<h3 data-number="5.0.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">5.0.1</span> Sequence attributes</h3>
<section id="reserved-sequence-attributes" class="level4" data-number="5.0.1.1">
<h4 data-number="5.0.1.1" class="anchored" data-anchor-id="reserved-sequence-attributes"><span class="header-section-number">5.0.1.1</span> Reserved sequence attributes</h4>
<section id="ali_dir" class="level5" data-number="5.0.1.1.1">
<h5 data-number="5.0.1.1.1" class="anchored" data-anchor-id="ali_dir"><span class="header-section-number">5.0.1.1.1</span> <code>ali_dir</code></h5>
<section id="type-string" class="level6" data-number="5.0.1.1.1.1">
<h6 data-number="5.0.1.1.1.1" class="anchored" data-anchor-id="type-string"><span class="header-section-number">5.0.1.1.1.1</span> Type : <code>string</code></h6>
<p>The attribute can contain 2 string values <code>"left"</code> or <code>"right".</code></p>
</section>
<section id="set-by-the-obipairing-tool" class="level6" data-number="4.0.1.1.1.2">
<h6 data-number="4.0.1.1.1.2" class="anchored" data-anchor-id="set-by-the-obipairing-tool"><span class="header-section-number">4.0.1.1.1.2</span> Set by the <em>obipairing</em> tool</h6>
<section id="set-by-the-obipairing-tool" class="level6" data-number="5.0.1.1.1.2">
<h6 data-number="5.0.1.1.1.2" class="anchored" data-anchor-id="set-by-the-obipairing-tool"><span class="header-section-number">5.0.1.1.1.2</span> Set by the <em>obipairing</em> tool</h6>
<p>The alignment generated by <em>obipairing</em> is a 3’-end gap free algorithm. Two cases can occur when aligning the forward and reverse reads. If the barcode is long enough, both the reads overlap only on their 3’ ends. In such case, the alignment direction <code>ali_dir</code> is set to <em>left</em>. If the barcode is shorter than the read length, the paired reads overlap by their 5’ ends, and the complete barcode is sequenced by both the reads. In that later case, <code>ali_dir</code> is set to <em>right</em>.</p>
</section>
</section>
<section id="ali_length" class="level5" data-number="4.0.1.1.2">
<h5 data-number="4.0.1.1.2" class="anchored" data-anchor-id="ali_length"><span class="header-section-number">4.0.1.1.2</span> <code>ali_length</code></h5>
<section id="set-by-the-obipairing-tool-1" class="level6" data-number="4.0.1.1.2.1">
<h6 data-number="4.0.1.1.2.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-1"><span class="header-section-number">4.0.1.1.2.1</span> Set by the <em>obipairing</em> tool</h6>
<section id="ali_length" class="level5" data-number="5.0.1.1.2">
<h5 data-number="5.0.1.1.2" class="anchored" data-anchor-id="ali_length"><span class="header-section-number">5.0.1.1.2</span> <code>ali_length</code></h5>
<section id="set-by-the-obipairing-tool-1" class="level6" data-number="5.0.1.1.2.1">
<h6 data-number="5.0.1.1.2.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-1"><span class="header-section-number">5.0.1.1.2.1</span> Set by the <em>obipairing</em> tool</h6>
<p>Length of the aligned parts when merging forward and reverse reads</p>
</section>
</section>
<section id="count-the-number-of-sequence-occurrences" class="level5" data-number="4.0.1.1.3">
<h5 data-number="4.0.1.1.3" class="anchored" data-anchor-id="count-the-number-of-sequence-occurrences"><span class="header-section-number">4.0.1.1.3</span> <code>count</code> : the number of sequence occurrences</h5>
<section id="set-by-the-obiuniq-tool" class="level6" data-number="4.0.1.1.3.1">
<h6 data-number="4.0.1.1.3.1" class="anchored" data-anchor-id="set-by-the-obiuniq-tool"><span class="header-section-number">4.0.1.1.3.1</span> Set by the <em>obiuniq</em> tool</h6>
<section id="count-the-number-of-sequence-occurrences" class="level5" data-number="5.0.1.1.3">
<h5 data-number="5.0.1.1.3" class="anchored" data-anchor-id="count-the-number-of-sequence-occurrences"><span class="header-section-number">5.0.1.1.3</span> <code>count</code> : the number of sequence occurrences</h5>
<section id="set-by-the-obiuniq-tool" class="level6" data-number="5.0.1.1.3.1">
<h6 data-number="5.0.1.1.3.1" class="anchored" data-anchor-id="set-by-the-obiuniq-tool"><span class="header-section-number">5.0.1.1.3.1</span> Set by the <em>obiuniq</em> tool</h6>
<p>The <code>count</code> attribute indicates how-many strictly identical sequences have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.</p>
</section>
<section id="getter-method-count" class="level6" data-number="4.0.1.1.3.2">
<h6 data-number="4.0.1.1.3.2" class="anchored" data-anchor-id="getter-method-count"><span class="header-section-number">4.0.1.1.3.2</span> Getter : method <code>Count()</code></h6>
<section id="getter-method-count" class="level6" data-number="5.0.1.1.3.2">
<h6 data-number="5.0.1.1.3.2" class="anchored" data-anchor-id="getter-method-count"><span class="header-section-number">5.0.1.1.3.2</span> Getter : method <code>Count()</code></h6>
<p>The <code>Count()</code> method allows to access to the count attribute as an integer value. If the <code>count</code> attribute is not defined for the given sequence, the value <em>1</em> is returned</p>
</section>
</section>
<section id="merged_" class="level5" data-number="4.0.1.1.4">
<h5 data-number="4.0.1.1.4" class="anchored" data-anchor-id="merged_"><span class="header-section-number">4.0.1.1.4</span> <code>merged_*</code></h5>
<section id="type-mapstringint" class="level6" data-number="4.0.1.1.4.1">
<h6 data-number="4.0.1.1.4.1" class="anchored" data-anchor-id="type-mapstringint"><span class="header-section-number">4.0.1.1.4.1</span> Type : <code>map[string]int</code></h6>
<section id="merged_" class="level5" data-number="5.0.1.1.4">
<h5 data-number="5.0.1.1.4" class="anchored" data-anchor-id="merged_"><span class="header-section-number">5.0.1.1.4</span> <code>merged_*</code></h5>
<section id="type-mapstringint" class="level6" data-number="5.0.1.1.4.1">
<h6 data-number="5.0.1.1.4.1" class="anchored" data-anchor-id="type-mapstringint"><span class="header-section-number">5.0.1.1.4.1</span> Type : <code>map[string]int</code></h6>
</section>
<section id="set-by-the-obiuniq-tool-1" class="level6" data-number="4.0.1.1.4.2">
<h6 data-number="4.0.1.1.4.2" class="anchored" data-anchor-id="set-by-the-obiuniq-tool-1"><span class="header-section-number">4.0.1.1.4.2</span> Set by the <em>obiuniq</em> tool</h6>
<section id="set-by-the-obiuniq-tool-1" class="level6" data-number="5.0.1.1.4.2">
<h6 data-number="5.0.1.1.4.2" class="anchored" data-anchor-id="set-by-the-obiuniq-tool-1"><span class="header-section-number">5.0.1.1.4.2</span> Set by the <em>obiuniq</em> tool</h6>
<p>The <code>-m</code> option of the <em>obiuniq</em> tools allows for keeping track of the distribution of the values stored in given attribute of interest. Often this option is used to summarise distribution of a sequence variant accross samples when <em>obiuniq</em> is run after running <em>obimultiplex</em>. The actual name of the attribute depends on the name of the monitored attribute. If <code>-m</code> option is used with the attribute <em>sample</em>, then this attribute names <em>merged_sample</em>.</p>
</section>
</section>
<section id="mode" class="level5" data-number="4.0.1.1.5">
<h5 data-number="4.0.1.1.5" class="anchored" data-anchor-id="mode"><span class="header-section-number">4.0.1.1.5</span> <code>mode</code></h5>
<section id="set-by-the-obipairing-tool-2" class="level6" data-number="4.0.1.1.5.1">
<h6 data-number="4.0.1.1.5.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-2"><span class="header-section-number">4.0.1.1.5.1</span> Set by the <em>obipairing</em> tool</h6>
<section id="mode" class="level5" data-number="5.0.1.1.5">
<h5 data-number="5.0.1.1.5" class="anchored" data-anchor-id="mode"><span class="header-section-number">5.0.1.1.5</span> <code>mode</code></h5>
<section id="set-by-the-obipairing-tool-2" class="level6" data-number="5.0.1.1.5.1">
<h6 data-number="5.0.1.1.5.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-2"><span class="header-section-number">5.0.1.1.5.1</span> Set by the <em>obipairing</em> tool</h6>
<p><strong><code>obitag_ref_index</code></strong></p>
</section>
<section id="set-by-the-obirefidx-tool." class="level6" data-number="4.0.1.1.5.2">
<h6 data-number="4.0.1.1.5.2" class="anchored" data-anchor-id="set-by-the-obirefidx-tool."><span class="header-section-number">4.0.1.1.5.2</span> Set by the <em>obirefidx</em> tool.</h6>
<section id="set-by-the-obirefidx-tool." class="level6" data-number="5.0.1.1.5.2">
<h6 data-number="5.0.1.1.5.2" class="anchored" data-anchor-id="set-by-the-obirefidx-tool."><span class="header-section-number">5.0.1.1.5.2</span> Set by the <em>obirefidx</em> tool.</h6>
<p>It resumes to which taxonomic annotation a match to that sequence must lead according to the number of differences existing between the query sequence and the reference sequence having that tag.</p>
</section>
<section id="getter-method-count-1" class="level6" data-number="4.0.1.1.5.3">
<h6 data-number="4.0.1.1.5.3" class="anchored" data-anchor-id="getter-method-count-1"><span class="header-section-number">4.0.1.1.5.3</span> Getter : method <code>Count()</code></h6>
<section id="getter-method-count-1" class="level6" data-number="5.0.1.1.5.3">
<h6 data-number="5.0.1.1.5.3" class="anchored" data-anchor-id="getter-method-count-1"><span class="header-section-number">5.0.1.1.5.3</span> Getter : method <code>Count()</code></h6>
</section>
</section>
<section id="pairing_mismatches" class="level5" data-number="4.0.1.1.6">
<h5 data-number="4.0.1.1.6" class="anchored" data-anchor-id="pairing_mismatches"><span class="header-section-number">4.0.1.1.6</span> <code>pairing_mismatches</code></h5>
<section id="set-by-the-obipairing-tool-3" class="level6" data-number="4.0.1.1.6.1">
<h6 data-number="4.0.1.1.6.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-3"><span class="header-section-number">4.0.1.1.6.1</span> Set by the <em>obipairing</em> tool</h6>
<section id="pairing_mismatches" class="level5" data-number="5.0.1.1.6">
<h5 data-number="5.0.1.1.6" class="anchored" data-anchor-id="pairing_mismatches"><span class="header-section-number">5.0.1.1.6</span> <code>pairing_mismatches</code></h5>
<section id="set-by-the-obipairing-tool-3" class="level6" data-number="5.0.1.1.6.1">
<h6 data-number="5.0.1.1.6.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-3"><span class="header-section-number">5.0.1.1.6.1</span> Set by the <em>obipairing</em> tool</h6>
</section>
</section>
<section id="score" class="level5" data-number="4.0.1.1.7">
<h5 data-number="4.0.1.1.7" class="anchored" data-anchor-id="score"><span class="header-section-number">4.0.1.1.7</span> <code>score</code></h5>
<section id="set-by-the-obipairing-tool-4" class="level6" data-number="4.0.1.1.7.1">
<h6 data-number="4.0.1.1.7.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-4"><span class="header-section-number">4.0.1.1.7.1</span> Set by the <em>obipairing</em> tool</h6>
<section id="score" class="level5" data-number="5.0.1.1.7">
<h5 data-number="5.0.1.1.7" class="anchored" data-anchor-id="score"><span class="header-section-number">5.0.1.1.7</span> <code>score</code></h5>
<section id="set-by-the-obipairing-tool-4" class="level6" data-number="5.0.1.1.7.1">
<h6 data-number="5.0.1.1.7.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-4"><span class="header-section-number">5.0.1.1.7.1</span> Set by the <em>obipairing</em> tool</h6>
</section>
</section>
<section id="score_norm" class="level5" data-number="4.0.1.1.8">
<h5 data-number="4.0.1.1.8" class="anchored" data-anchor-id="score_norm"><span class="header-section-number">4.0.1.1.8</span> <code>score_norm</code></h5>
<section id="set-by-the-obipairing-tool-5" class="level6" data-number="4.0.1.1.8.1">
<h6 data-number="4.0.1.1.8.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-5"><span class="header-section-number">4.0.1.1.8.1</span> Set by the <em>obipairing</em> tool</h6>
<section id="score_norm" class="level5" data-number="5.0.1.1.8">
<h5 data-number="5.0.1.1.8" class="anchored" data-anchor-id="score_norm"><span class="header-section-number">5.0.1.1.8</span> <code>score_norm</code></h5>
<section id="set-by-the-obipairing-tool-5" class="level6" data-number="5.0.1.1.8.1">
<h6 data-number="5.0.1.1.8.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-5"><span class="header-section-number">5.0.1.1.8.1</span> Set by the <em>obipairing</em> tool</h6>
</section>
@@ -373,7 +378,7 @@ window.document.addEventListener("DOMContentLoaded", function (event) {
<nav class="page-navigation">
<div class="nav-page nav-page-previous">
<a href="./library.html" class="pagination-link">
<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">The GO <em>OBITools</em> library</span></span>
<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">The GO <em>OBITools</em> library</span></span>
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