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updated docs
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lskatz committed Oct 14, 2023
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17 changes: 8 additions & 9 deletions docs/fasten_repair/index.html
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Expand Up @@ -18,22 +18,21 @@ <h2 id="usage" class="section-header"><a href="#usage">Usage</a></h2><div class=
Minimum quality allowed
--remove-info Remove fasten_inspect headers
-m, --mode STRING Either repair or panic. If panic, then the binary will
panic when the first issue comes up. Default:repair</code></pre></div><h2 id="methods-of-repair" class="section-header"><a href="#methods-of-repair">Methods of repair</a></h2>
panic when the first issue comes up. Default:repair</code></pre></div><h2 id="methods-of-repair" class="section-header"><a href="#methods-of-repair">Methods of repair</a></h2><h2 id="repair-mode" class="section-header"><a href="#repair-mode">Repair mode</a></h2>
<p>If you choose <code>--mode repair</code>, then this is the expected behavior</p>
<ul>
<li>Mismatched seq and qual lengths: seq or qual length will be truncated</li>
<li>R1 or R2 not passing: then the other (R1 or R2) will also not pass and they will not be
printed.</li>
</ul>
<h2 id="panic" class="section-header"><a href="#panic">Panic</a></h2>
<p>If the sequences are not repaired but there is still an issue, the program might still panic:</p>
<h2 id="panic-mode" class="section-header"><a href="#panic-mode">Panic mode</a></h2>
<ul>
<li>seq length &lt; min length (TODO when implementing PE reads)</li>
<li>avg qual &lt; min qual (TODO when implementing PE reads)</li>
<li>invalid characters in seq (TODO when implementing PE reads)</li>
<li>invalid characters in qual (TODO when implementing PE reads)</li>
<li><code>@</code> not present in first character of the entry (TODO when implementing PE reads)</li>
<li><code>+</code> not present in the first character of the third line (TODO when implementing PE reads)</li>
<li>seq length &lt; min length </li>
<li>avg qual &lt; min qual </li>
<li>invalid characters in seq </li>
<li>invalid characters in qual </li>
<li><code>@</code> not present in first character of the entry </li>
<li><code>+</code> not present in the first character of the third line </li>
</ul>
</div></details><h2 id="functions" class="small-section-header"><a href="#functions">Functions</a></h2>
<div class="item-table"><div class="item-row"><div class="item-left module-item"><a class="fn" href="fn.main.html" title="fasten_repair::main fn">main</a></div><div class="item-right docblock-short"></div></div><div class="item-row"><div class="item-left module-item"><a class="fn" href="fn.repair_one_read.html" title="fasten_repair::repair_one_read fn">repair_one_read</a></div><div class="item-right docblock-short"><p>Repair exactly one read</p>
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6 changes: 3 additions & 3 deletions docs/settings.html
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<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="generator" content="rustdoc"><meta name="description" content="Settings of Rustdoc"><meta name="keywords" content="rust, rustlang, rust-lang"><title>Rustdoc settings</title><link rel="preload" as="font" type="font/woff2" crossorigin href="./SourceSerif4-Regular.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./FiraSans-Regular.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./FiraSans-Medium.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./SourceCodePro-Regular.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./SourceSerif4-Bold.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="./SourceCodePro-Semibold.ttf.woff2"><link rel="stylesheet" type="text/css" href="./normalize.css"><link rel="stylesheet" type="text/css" href="./rustdoc.css" id="mainThemeStyle"><link rel="stylesheet" type="text/css" href="./ayu.css" disabled><link rel="stylesheet" type="text/css" href="./dark.css" disabled><link rel="stylesheet" type="text/css" href="./light.css" id="themeStyle"><script id="default-settings" ></script><script src="./storage.js"></script><script src="./crates.js"></script><script defer src="./main.js"></script>
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<noscript><link rel="stylesheet" href="./noscript.css"></noscript><link rel="alternate icon" type="image/png" href="./favicon-16x16.png"><link rel="alternate icon" type="image/png" href="./favicon-32x32.png"><link rel="icon" type="image/svg+xml" href="./favicon.svg"></head><body class="rustdoc mod"><!--[if lte IE 11]><div class="warning">This old browser is unsupported and will most likely display funky things.</div><![endif]--><nav class="sidebar"><div class="sidebar-menu" role="button">&#9776;</div><a class="sidebar-logo" href="./fasten_sort/index.html"><div class="logo-container"><img class="rust-logo" src="./rust-logo.png" alt="logo"></div>
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18 changes: 9 additions & 9 deletions docs/src/fasten_repair/fasten_repair.rs.html
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Expand Up @@ -347,22 +347,22 @@
<span class="doccomment">//!</span>
<span class="doccomment">//! # Methods of repair</span>
<span class="doccomment">//!</span>
<span class="doccomment">//! # Repair mode</span>
<span class="doccomment">//!</span>
<span class="doccomment">//! If you choose `--mode repair`, then this is the expected behavior</span>
<span class="doccomment">//!</span>
<span class="doccomment">//! * Mismatched seq and qual lengths: seq or qual length will be truncated</span>
<span class="doccomment">//! * R1 or R2 not passing: then the other (R1 or R2) will also not pass and they will not be</span>
<span class="doccomment">//! printed.</span>
<span class="doccomment">//!</span>
<span class="doccomment">//! # Panic</span>
<span class="doccomment">//!</span>
<span class="doccomment">//! If the sequences are not repaired but there is still an issue, the program might still panic:</span>
<span class="doccomment">//! # Panic mode</span>
<span class="doccomment">//!</span>
<span class="doccomment">//! * seq length &lt; min length (TODO when implementing PE reads)</span>
<span class="doccomment">//! * avg qual &lt; min qual (TODO when implementing PE reads)</span>
<span class="doccomment">//! * invalid characters in seq (TODO when implementing PE reads)</span>
<span class="doccomment">//! * invalid characters in qual (TODO when implementing PE reads)</span>
<span class="doccomment">//! * `@` not present in first character of the entry (TODO when implementing PE reads)</span>
<span class="doccomment">//! * `+` not present in the first character of the third line (TODO when implementing PE reads)</span>
<span class="doccomment">//! * seq length &lt; min length </span>
<span class="doccomment">//! * avg qual &lt; min qual </span>
<span class="doccomment">//! * invalid characters in seq </span>
<span class="doccomment">//! * invalid characters in qual </span>
<span class="doccomment">//! * `@` not present in first character of the entry </span>
<span class="doccomment">//! * `+` not present in the first character of the third line </span>
<span class="doccomment">//! </span>

<span class="kw">extern</span> <span class="kw">crate</span> <span class="ident">getopts</span>;
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