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‎javadoc/allclasses-index.html‎

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<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<!-- Generated by javadoc (21) -->
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<title>All Classes and Interfaces (MUSIAL v2.3.10 API)</title>
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
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<meta name="description" content="class index">
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<meta name="generator" content="javadoc/AllClassesIndexWriter">
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<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
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<link rel="stylesheet" type="text/css" href="script-dir/jquery-ui.min.css" title="Style">
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<script type="text/javascript" src="script.js"></script>
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<script type="text/javascript" src="script-dir/jquery-3.7.1.min.js"></script>
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<script type="text/javascript" src="script-dir/jquery-ui.min.js"></script>
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</head>
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<body class="all-classes-index-page">
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<script type="text/javascript">var pathtoroot = "./";
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loadScripts(document, 'script');</script>
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<noscript>
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<div>JavaScript is disabled on your browser.</div>
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</noscript>
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<div class="flex-box">
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<header role="banner" class="flex-header">
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<nav role="navigation">
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<!-- ========= START OF TOP NAVBAR ======= -->
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<div class="top-nav" id="navbar-top"><button id="navbar-toggle-button" aria-controls="navbar-top" aria-expanded="false" aria-label="Toggle navigation links"><span class="nav-bar-toggle-icon">&nbsp;</span><span class="nav-bar-toggle-icon">&nbsp;</span><span class="nav-bar-toggle-icon">&nbsp;</span></button>
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<div class="skip-nav"><a href="#skip-navbar-top" title="Skip navigation links">Skip navigation links</a></div>
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<ul id="navbar-top-firstrow" class="nav-list" title="Navigation">
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<li><a href="index.html">Overview</a></li>
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<li>Package</li>
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<li>Class</li>
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<li><a href="overview-tree.html">Tree</a></li>
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<li><a href="index-all.html">Index</a></li>
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<li><a href="help-doc.html#all-classes">Help</a></li>
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</ul>
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</div>
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<div class="sub-nav">
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<div id="navbar-sub-list"></div>
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<div class="nav-list-search"><a href="search.html">SEARCH</a>
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<input type="text" id="search-input" disabled placeholder="Search">
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<input type="reset" id="reset-button" disabled value="reset">
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<!-- ========= END OF TOP NAVBAR ========= -->
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<span class="skip-nav" id="skip-navbar-top"></span></nav>
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</header>
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<div class="flex-content">
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<main role="main">
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<div class="header">
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<h1 title="All Classes and Interfaces" class="title">All Classes and Interfaces</h1>
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</div>
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<div id="all-classes-table">
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<div class="table-tabs" role="tablist" aria-orientation="horizontal"><button id="all-classes-table-tab0" role="tab" aria-selected="true" aria-controls="all-classes-table.tabpanel" tabindex="0" onkeydown="switchTab(event)" onclick="show('all-classes-table', 'all-classes-table', 2)" class="active-table-tab">All Classes and Interfaces</button><button id="all-classes-table-tab2" role="tab" aria-selected="false" aria-controls="all-classes-table.tabpanel" tabindex="-1" onkeydown="switchTab(event)" onclick="show('all-classes-table', 'all-classes-table-tab2', 2)" class="table-tab">Classes</button><button id="all-classes-table-tab3" role="tab" aria-selected="false" aria-controls="all-classes-table.tabpanel" tabindex="-1" onkeydown="switchTab(event)" onclick="show('all-classes-table', 'all-classes-table-tab3', 2)" class="table-tab">Enum Classes</button><button id="all-classes-table-tab5" role="tab" aria-selected="false" aria-controls="all-classes-table.tabpanel" tabindex="-1" onkeydown="switchTab(event)" onclick="show('all-classes-table', 'all-classes-table-tab5', 2)" class="table-tab">Exception Classes</button></div>
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<div id="all-classes-table.tabpanel" role="tabpanel" aria-labelledby="all-classes-table-tab0">
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<div class="summary-table two-column-summary">
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<div class="table-header col-first">Class</div>
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<div class="table-header col-last">Description</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="utility/AlleleAnalyzer.html" title="class in utility">AlleleAnalyzer</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Implements static methods for allele analysis to infer proteoforms.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="cli/BuildConfiguration.html" title="class in cli">BuildConfiguration</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Parse parameters for `build` task.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="utility/CL.html" title="class in utility">CL</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Implements static methods to run command line commands.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="cli/CLIParser.html" title="class in cli">CLIParser</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Parses command line interface arguments.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="utility/Compression.html" title="class in utility">Compression</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Implements static methods to compress <a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link"><code>String</code></a> content using the <a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/util/zip/package-summary.html" class="external-link"><code>java.util.zip</code></a> library.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="main/Constants.html" title="class in main">Constants</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Collection of common property keys used for annotations.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/Feature.html" title="class in datastructure">Feature</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Container to store representation of a reference sequence location that is subject to analysis.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/FeatureCoding.html" title="class in datastructure">FeatureCoding</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Extension of the <a href="datastructure/Feature.html" title="class in datastructure"><code>Feature</code></a> class to represent coding features.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/Form.html" title="class in datastructure">Form</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Container to store a biological variation of a feature, i.e., an allele of a gene or proteoform of a protein.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/InfoContainer.html" title="class in datastructure">InfoContainer</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Interface for meta-information storage.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="utility/IO.html" title="class in utility">IO</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">This class comprises static methods used for reading and writing files.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="utility/Logger.html" title="class in utility">Logger</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Comprises static methods used for CL logging.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="main/Musial.html" title="class in main">Musial</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Main class of MUSIAL (MUlti Sample varIant AnaLysis), a tool to calculate SNV, gene, and whole genome alignments,
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together with other relevant statistics based on vcf files.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab5"><a href="exceptions/MusialException.html" title="class in exceptions">MusialException</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab5">
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<div class="block">Exception thrown if any data generation or storage process is incorrect in the context of the software, e.g.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/MusialStorage.html" title="class in datastructure">MusialStorage</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Main data structure to store information about variants wrt.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/MusialStorageFactory.html" title="class in datastructure">MusialStorageFactory</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Factory class for <a href="datastructure/MusialStorage.html" title="class in datastructure"><code>MusialStorage</code></a> instances.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/MusialStorageParameters.html" title="class in datastructure">MusialStorageParameters</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Stores parameters used for variant call filtering.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/OccurrenceContainer.html" title="class in datastructure">OccurrenceContainer</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Interface for sample occurrence storage.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/Sample.html" title="class in datastructure">Sample</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Representation of a sample, i.e., variant calls from a single biological sample.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="utility/SampleAnalyzer.html" title="class in utility">SampleAnalyzer</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Implements static methods to run sample/.vcf analysis.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="utility/SequenceOperations.html" title="class in utility">SequenceOperations</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Implements static methods for sequence operations, such as inversion, translation, and alignment.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab3"><a href="utility/SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES.html" title="enum class in utility">SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab3">
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<div class="block">Enum to store different modes to handle prefix gaps for global sequence alignment.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="utility/SnpEffAnnotator.html" title="class in utility">SnpEffAnnotator</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Implements static methods to run SnpEff locally via command line.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab3"><a href="main/Tasks.html" title="enum class in main">Tasks</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab3">
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<div class="block"><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/Enum.html" title="class or interface in java.lang" class="external-link"><code>Enum</code></a> specifying tasks of MUSIAL to choose from.</div>
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</div>
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<div class="col-first even-row-color all-classes-table all-classes-table-tab2"><a href="utility/Validation.html" title="class in utility">Validation</a></div>
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<div class="col-last even-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Implements static methods used for validating input parameters.</div>
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</div>
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<div class="col-first odd-row-color all-classes-table all-classes-table-tab2"><a href="datastructure/VariantInformation.html" title="class in datastructure">VariantInformation</a></div>
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<div class="col-last odd-row-color all-classes-table all-classes-table-tab2">
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<div class="block">Container to store annotations and information of a single variant on a feature.</div>
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</div>
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</div>
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</div>
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</div>
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</main>
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</div>
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</div>
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</body>
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</html>

‎javadoc/allpackages-index.html‎

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<!DOCTYPE HTML>
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<html lang="en">
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<head>
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<!-- Generated by javadoc (21) -->
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<title>All Packages (MUSIAL v2.3.10 API)</title>
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
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<meta name="description" content="package index">
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<meta name="generator" content="javadoc/AllPackagesIndexWriter">
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<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
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<link rel="stylesheet" type="text/css" href="script-dir/jquery-ui.min.css" title="Style">
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<script type="text/javascript" src="script.js"></script>
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<script type="text/javascript" src="script-dir/jquery-3.7.1.min.js"></script>
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<script type="text/javascript" src="script-dir/jquery-ui.min.js"></script>
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</head>
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<body class="all-packages-index-page">
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<script type="text/javascript">var pathtoroot = "./";
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loadScripts(document, 'script');</script>
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<noscript>
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<div>JavaScript is disabled on your browser.</div>
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</noscript>
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<div class="flex-box">
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<header role="banner" class="flex-header">
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<nav role="navigation">
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<!-- ========= START OF TOP NAVBAR ======= -->
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<div class="top-nav" id="navbar-top"><button id="navbar-toggle-button" aria-controls="navbar-top" aria-expanded="false" aria-label="Toggle navigation links"><span class="nav-bar-toggle-icon">&nbsp;</span><span class="nav-bar-toggle-icon">&nbsp;</span><span class="nav-bar-toggle-icon">&nbsp;</span></button>
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<div class="skip-nav"><a href="#skip-navbar-top" title="Skip navigation links">Skip navigation links</a></div>
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<ul id="navbar-top-firstrow" class="nav-list" title="Navigation">
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<li><a href="index.html">Overview</a></li>
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<li>Package</li>
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<li>Class</li>
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<li><a href="overview-tree.html">Tree</a></li>
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<li><a href="index-all.html">Index</a></li>
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<li><a href="help-doc.html#all-packages">Help</a></li>
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</ul>
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</div>
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<div class="sub-nav">
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<div id="navbar-sub-list"></div>
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<div class="nav-list-search"><a href="search.html">SEARCH</a>
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<input type="text" id="search-input" disabled placeholder="Search">
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<input type="reset" id="reset-button" disabled value="reset">
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</div>
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</div>
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<!-- ========= END OF TOP NAVBAR ========= -->
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<span class="skip-nav" id="skip-navbar-top"></span></nav>
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</header>
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<div class="flex-content">
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<main role="main">
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<div class="header">
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<h1 title="All&amp;nbsp;Packages" class="title">All&nbsp;Packages</h1>
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</div>
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<div class="caption"><span>Package Summary</span></div>
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<div class="summary-table two-column-summary">
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<div class="table-header col-first">Package</div>
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<div class="table-header col-last">Description</div>
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<div class="col-first even-row-color"><a href="cli/package-summary.html">cli</a></div>
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<div class="col-last even-row-color">
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<div class="block">Comprises classes to parse command line interface arguments for each task.</div>
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</div>
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<div class="col-first odd-row-color"><a href="datastructure/package-summary.html">datastructure</a></div>
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<div class="col-last odd-row-color">
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<div class="block">Comprises all classes that constitute the variant call storage datastructures of MUSIAL.</div>
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</div>
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<div class="col-first even-row-color"><a href="exceptions/package-summary.html">exceptions</a></div>
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<div class="col-last even-row-color">
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<div class="block">Comprises classes that extend the <a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/Exception.html" title="class or interface in java.lang" class="external-link"><code>Exception</code></a> class.</div>
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</div>
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<div class="col-first odd-row-color"><a href="main/package-summary.html">main</a></div>
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<div class="col-last odd-row-color">
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<div class="block">Comprises the main class of MUSIAL.</div>
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</div>
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<div class="col-first even-row-color"><a href="utility/package-summary.html">utility</a></div>
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<div class="col-last even-row-color">
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<div class="block">Comprises classes that mainly implement static methods, which are used by MUSIAL modules.</div>
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</div>
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</div>
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</main>
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</div>
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</div>
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</body>
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</html>

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