mirror of
https://github.com/metabarcoding/obitools4.git
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Refactoring codes for removing buffer size options. An some other changes...
Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
This commit is contained in:
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doc/build/_book/annexes.html
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@@ -20,6 +20,69 @@ ul.task-list li input[type="checkbox"] {
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margin: 0 0.8em 0.2em -1.6em;
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vertical-align: middle;
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}
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pre > code.sourceCode { white-space: pre; position: relative; }
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pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
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pre > code.sourceCode > span:empty { height: 1.2em; }
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.sourceCode { overflow: visible; }
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code.sourceCode > span { color: inherit; text-decoration: inherit; }
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div.sourceCode { margin: 1em 0; }
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pre.sourceCode { margin: 0; }
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@media screen {
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div.sourceCode { overflow: auto; }
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}
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@media print {
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pre > code.sourceCode { white-space: pre-wrap; }
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pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
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}
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pre.numberSource code
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{ counter-reset: source-line 0; }
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pre.numberSource code > span
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{ position: relative; left: -4em; counter-increment: source-line; }
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pre.numberSource code > span > a:first-child::before
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{ content: counter(source-line);
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position: relative; left: -1em; text-align: right; vertical-align: baseline;
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border: none; display: inline-block;
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-webkit-touch-callout: none; -webkit-user-select: none;
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-khtml-user-select: none; -moz-user-select: none;
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-ms-user-select: none; user-select: none;
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padding: 0 4px; width: 4em;
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color: #aaaaaa;
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}
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pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
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div.sourceCode
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{ }
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@media screen {
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pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
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}
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code span.al { color: #ff0000; font-weight: bold; } /* Alert */
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code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
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code span.at { color: #7d9029; } /* Attribute */
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code span.bn { color: #40a070; } /* BaseN */
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code span.bu { color: #008000; } /* BuiltIn */
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code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
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code span.ch { color: #4070a0; } /* Char */
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code span.cn { color: #880000; } /* Constant */
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code span.co { color: #60a0b0; font-style: italic; } /* Comment */
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code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
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code span.do { color: #ba2121; font-style: italic; } /* Documentation */
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code span.dt { color: #902000; } /* DataType */
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code span.dv { color: #40a070; } /* DecVal */
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code span.er { color: #ff0000; font-weight: bold; } /* Error */
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code span.ex { } /* Extension */
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code span.fl { color: #40a070; } /* Float */
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code span.fu { color: #06287e; } /* Function */
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code span.im { color: #008000; font-weight: bold; } /* Import */
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code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
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code span.kw { color: #007020; font-weight: bold; } /* Keyword */
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code span.op { color: #666666; } /* Operator */
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code span.ot { color: #007020; } /* Other */
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code span.pp { color: #bc7a00; } /* Preprocessor */
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code span.sc { color: #4070a0; } /* SpecialChar */
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code span.ss { color: #bb6688; } /* SpecialString */
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code span.st { color: #4070a0; } /* String */
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code span.va { color: #19177c; } /* Variable */
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code span.vs { color: #4070a0; } /* VerbatimString */
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code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
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</style>
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@@ -215,7 +278,7 @@ ul.task-list li input[type="checkbox"] {
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<h2 id="toc-title">Table of contents</h2>
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<ul>
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<li><a href="#sequence-attributes" id="toc-sequence-attributes" class="nav-link active" data-scroll-target="#sequence-attributes"><span class="toc-section-number">A.0.1</span> Sequence attributes</a></li>
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<li><a href="#sequence-attributes" id="toc-sequence-attributes" class="nav-link active" data-scroll-target="#sequence-attributes"><span class="toc-section-number">A.1</span> Sequence attributes</a></li>
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</ul>
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</nav>
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</div>
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@@ -239,84 +302,82 @@ ul.task-list li input[type="checkbox"] {
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</header>
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<section id="sequence-attributes" class="level3" data-number="A.0.1">
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<h3 data-number="A.0.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">A.0.1</span> Sequence attributes</h3>
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<section id="reserved-sequence-attributes" class="level4" data-number="A.0.1.1">
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<h4 data-number="A.0.1.1" class="anchored" data-anchor-id="reserved-sequence-attributes"><span class="header-section-number">A.0.1.1</span> Reserved sequence attributes</h4>
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<section id="ali_dir" class="level5" data-number="A.0.1.1.1">
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<h5 data-number="A.0.1.1.1" class="anchored" data-anchor-id="ali_dir"><span class="header-section-number">A.0.1.1.1</span> <code>ali_dir</code></h5>
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<section id="type-string" class="level6" data-number="A.0.1.1.1.1">
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<h6 data-number="A.0.1.1.1.1" class="anchored" data-anchor-id="type-string"><span class="header-section-number">A.0.1.1.1.1</span> Type : <code>string</code></h6>
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<p>The attribute can contain 2 string values <code>"left"</code> or <code>"right".</code></p>
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</section>
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<section id="set-by-the-obipairing-tool" class="level6" data-number="A.0.1.1.1.2">
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<h6 data-number="A.0.1.1.1.2" class="anchored" data-anchor-id="set-by-the-obipairing-tool"><span class="header-section-number">A.0.1.1.1.2</span> Set by the <em>obipairing</em> tool</h6>
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<section id="sequence-attributes" class="level2" data-number="A.1">
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<h2 data-number="A.1" class="anchored" data-anchor-id="sequence-attributes"><span class="header-section-number">A.1</span> Sequence attributes</h2>
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<p><strong>ali_dir (<code>string</code>)</strong></p>
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<ul>
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<li>Set by the <em>obipairing</em> tool</li>
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<li>The attribute can contain 2 string values <code>left</code> or <code>right</code>.</li>
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</ul>
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<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>
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</section>
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</section>
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<section id="ali_length" class="level5" data-number="A.0.1.1.2">
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<h5 data-number="A.0.1.1.2" class="anchored" data-anchor-id="ali_length"><span class="header-section-number">A.0.1.1.2</span> <code>ali_length</code></h5>
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<section id="set-by-the-obipairing-tool-1" class="level6" data-number="A.0.1.1.2.1">
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<h6 data-number="A.0.1.1.2.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-1"><span class="header-section-number">A.0.1.1.2.1</span> Set by the <em>obipairing</em> tool</h6>
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<p><strong>ali_length (<code>int</code>)</strong></p>
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<ul>
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<li>Set by the <em>obipairing</em> tool</li>
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</ul>
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<p>Length of the aligned parts when merging forward and reverse reads</p>
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</section>
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</section>
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<section id="count-the-number-of-sequence-occurrences" class="level5" data-number="A.0.1.1.3">
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<h5 data-number="A.0.1.1.3" class="anchored" data-anchor-id="count-the-number-of-sequence-occurrences"><span class="header-section-number">A.0.1.1.3</span> <code>count</code> : the number of sequence occurrences</h5>
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<section id="set-by-the-obiuniq-tool" class="level6" data-number="A.0.1.1.3.1">
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<h6 data-number="A.0.1.1.3.1" class="anchored" data-anchor-id="set-by-the-obiuniq-tool"><span class="header-section-number">A.0.1.1.3.1</span> Set by the <em>obiuniq</em> tool</h6>
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<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>
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</section>
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<section id="getter-method-count" class="level6" data-number="A.0.1.1.3.2">
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<h6 data-number="A.0.1.1.3.2" class="anchored" data-anchor-id="getter-method-count"><span class="header-section-number">A.0.1.1.3.2</span> Getter : method <code>Count()</code></h6>
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<p><strong>count (<code>int</code>)</strong></p>
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<ul>
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<li>Set by the <em>obiuniq</em> tool</li>
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<li>Getter : method <code>Count()</code></li>
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<li>Setter : method <code>SetCount(int)</code></li>
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</ul>
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<p>The <code>count</code> attribute indicates how-many strictly identical reads 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>
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<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>
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</section>
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</section>
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<section id="merged_" class="level5" data-number="A.0.1.1.4">
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<h5 data-number="A.0.1.1.4" class="anchored" data-anchor-id="merged_"><span class="header-section-number">A.0.1.1.4</span> <code>merged_*</code></h5>
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<section id="type-mapstringint" class="level6" data-number="A.0.1.1.4.1">
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<h6 data-number="A.0.1.1.4.1" class="anchored" data-anchor-id="type-mapstringint"><span class="header-section-number">A.0.1.1.4.1</span> Type : <code>map[string]int</code></h6>
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</section>
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<section id="set-by-the-obiuniq-tool-1" class="level6" data-number="A.0.1.1.4.2">
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<h6 data-number="A.0.1.1.4.2" class="anchored" data-anchor-id="set-by-the-obiuniq-tool-1"><span class="header-section-number">A.0.1.1.4.2</span> Set by the <em>obiuniq</em> tool</h6>
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<p><strong>merged_* (<code>map[string]int</code>)</strong></p>
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<ul>
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<li>Set by the <em>obiuniq</em> tool</li>
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</ul>
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<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>
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</section>
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</section>
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<section id="mode" class="level5" data-number="A.0.1.1.5">
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<h5 data-number="A.0.1.1.5" class="anchored" data-anchor-id="mode"><span class="header-section-number">A.0.1.1.5</span> <code>mode</code></h5>
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<section id="set-by-the-obipairing-tool-2" class="level6" data-number="A.0.1.1.5.1">
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<h6 data-number="A.0.1.1.5.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-2"><span class="header-section-number">A.0.1.1.5.1</span> Set by the <em>obipairing</em> tool</h6>
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<p><strong><code>obitag_ref_index</code></strong></p>
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</section>
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<section id="set-by-the-obirefidx-tool." class="level6" data-number="A.0.1.1.5.2">
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<h6 data-number="A.0.1.1.5.2" class="anchored" data-anchor-id="set-by-the-obirefidx-tool."><span class="header-section-number">A.0.1.1.5.2</span> Set by the <em>obirefidx</em> tool.</h6>
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<p><strong>mode (<code>string</code>)</strong></p>
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<ul>
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<li>Set by the <em>obipairing</em> tool</li>
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<li>The attribute can contain 2 string values <code>join</code> or <code>alignment</code>.</li>
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</ul>
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<p><strong>obitag_ref_index (<code>map[string]string</code>)</strong></p>
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<ul>
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<li>Set by the <em>obirefidx</em> tool.</li>
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</ul>
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<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>
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</section>
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<section id="getter-method-count-1" class="level6" data-number="A.0.1.1.5.3">
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<h6 data-number="A.0.1.1.5.3" class="anchored" data-anchor-id="getter-method-count-1"><span class="header-section-number">A.0.1.1.5.3</span> Getter : method <code>Count()</code></h6>
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</section>
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</section>
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<section id="pairing_mismatches" class="level5" data-number="A.0.1.1.6">
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<h5 data-number="A.0.1.1.6" class="anchored" data-anchor-id="pairing_mismatches"><span class="header-section-number">A.0.1.1.6</span> <code>pairing_mismatches</code></h5>
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<section id="set-by-the-obipairing-tool-3" class="level6" data-number="A.0.1.1.6.1">
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<h6 data-number="A.0.1.1.6.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-3"><span class="header-section-number">A.0.1.1.6.1</span> Set by the <em>obipairing</em> tool</h6>
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</section>
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</section>
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<section id="score" class="level5" data-number="A.0.1.1.7">
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<h5 data-number="A.0.1.1.7" class="anchored" data-anchor-id="score"><span class="header-section-number">A.0.1.1.7</span> <code>score</code></h5>
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<section id="set-by-the-obipairing-tool-4" class="level6" data-number="A.0.1.1.7.1">
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<h6 data-number="A.0.1.1.7.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-4"><span class="header-section-number">A.0.1.1.7.1</span> Set by the <em>obipairing</em> tool</h6>
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</section>
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</section>
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<section id="score_norm" class="level5" data-number="A.0.1.1.8">
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<h5 data-number="A.0.1.1.8" class="anchored" data-anchor-id="score_norm"><span class="header-section-number">A.0.1.1.8</span> <code>score_norm</code></h5>
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<section id="set-by-the-obipairing-tool-5" class="level6" data-number="A.0.1.1.8.1">
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<h6 data-number="A.0.1.1.8.1" class="anchored" data-anchor-id="set-by-the-obipairing-tool-5"><span class="header-section-number">A.0.1.1.8.1</span> Set by the <em>obipairing</em> tool</h6>
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<div class="sourceCode" id="cb1"><pre class="sourceCode json code-with-copy"><code class="sourceCode json"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> <span class="fu">{</span><span class="dt">"0"</span><span class="fu">:</span><span class="st">"9606@Homo sapiens@species"</span><span class="fu">,</span></span>
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<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="dt">"2"</span><span class="fu">:</span><span class="st">"207598@Homininae@subfamily"</span><span class="fu">,</span></span>
|
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<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="dt">"3"</span><span class="fu">:</span><span class="st">"9604@Hominidae@family"</span><span class="fu">,</span></span>
|
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<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="dt">"8"</span><span class="fu">:</span><span class="st">"314295@Hominoidea@superfamily"</span><span class="fu">,</span></span>
|
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<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> <span class="dt">"10"</span><span class="fu">:</span><span class="st">"9526@Catarrhini@parvorder"</span><span class="fu">,</span></span>
|
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<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="dt">"12"</span><span class="fu">:</span><span class="st">"1437010@Boreoeutheria@clade"</span><span class="fu">,</span></span>
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<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> <span class="dt">"16"</span><span class="fu">:</span><span class="st">"9347@Eutheria@clade"</span><span class="fu">,</span></span>
|
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<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="dt">"17"</span><span class="fu">:</span><span class="st">"40674@Mammalia@class"</span><span class="fu">,</span></span>
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<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="dt">"22"</span><span class="fu">:</span><span class="st">"117571@Euteleostomi@clade"</span><span class="fu">,</span></span>
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<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="dt">"25"</span><span class="fu">:</span><span class="st">"7776@Gnathostomata@clade"</span><span class="fu">,</span></span>
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<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> <span class="dt">"29"</span><span class="fu">:</span><span class="st">"33213@Bilateria@clade"</span><span class="fu">,</span></span>
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<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="dt">"30"</span><span class="fu">:</span><span class="st">"6072@Eumetazoa@clade"</span><span class="fu">}</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
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<p><strong>pairing_mismatches (<code>map[string]string</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>seq_a_single (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
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<p><strong>seq_ab_match (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
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<p><strong>seq_b_single (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>score (<code>int</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
</ul>
|
||||
<p><strong>score_norm (<code>float</code>)</strong></p>
|
||||
<ul>
|
||||
<li>Set by the <em>obipairing</em> tool</li>
|
||||
<li>The value ranges between 0 and 1.</li>
|
||||
</ul>
|
||||
<p>Score of the alignment between forward and reverse reads expressed as a fraction of identity.</p>
|
||||
|
||||
|
||||
</section>
|
||||
</section>
|
||||
</section>
|
||||
</section>
|
||||
|
||||
</main> <!-- /main -->
|
||||
|
||||
Reference in New Issue
Block a user