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Fasten metrics bug fix (#46)
* f64 * fixed phred score * fixed test for phred score * updated answers for corrected phred scores * benchmark_metrics * benchmark_metrics * docs and some new gitignore * speed up fasten_metrics; make very large file for metrics benchmark * make large test file larger
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‎.gitignore‎

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testdata/R2.large.fastq
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testdata/shuffled.large.fastq.gz
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testdata/shuffled.sorted.fastq.gz
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testdata/shuffled.sorted.largest.fastq.gz
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# some of Lee's
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/*.fastq.gz
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/*.fq.gz
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‎Cargo.toml‎

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[package]
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name = "fasten"
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version = "0.8.9"
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version = "0.9.0"
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authors = ["Lee Katz <gzu2@cdc.gov>"]
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#license-file = "LICENSE"
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license = "MIT"

‎docs/fasten/all.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="List of all items in this crate"><title>List of all items in this crate</title><script>if(window.location.protocol!=="file:")document.head.insertAdjacentHTML("beforeend","SourceSerif4-Regular-46f98efaafac5295.ttf.woff2,FiraSans-Regular-018c141bf0843ffd.woff2,FiraSans-Medium-8f9a781e4970d388.woff2,SourceCodePro-Regular-562dcc5011b6de7d.ttf.woff2,SourceCodePro-Semibold-d899c5a5c4aeb14a.ttf.woff2".split(",").map(f=>`<link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/${f}">`).join(""))</script><link rel="stylesheet" href="../static.files/normalize-76eba96aa4d2e634.css"><link rel="stylesheet" href="../static.files/rustdoc-b0742ba02757f159.css"><meta name="rustdoc-vars" data-root-path="../" data-static-root-path="../static.files/" data-current-crate="fasten" data-themes="" data-resource-suffix="" data-rustdoc-version="1.83.0 (90b35a623 2024-11-26)" data-channel="1.83.0" data-search-js="search-f0d225181b97f9a4.js" data-settings-js="settings-805db61a62df4bd2.js" ><script src="../static.files/storage-1d39b6787ed640ff.js"></script><script defer src="../static.files/main-f070b9041d14864c.js"></script><noscript><link rel="stylesheet" href="../static.files/noscript-0111fcff984fae8f.css"></noscript><link rel="alternate icon" type="image/png" href="../static.files/favicon-32x32-422f7d1d52889060.png"><link rel="icon" type="image/svg+xml" href="../static.files/favicon-2c020d218678b618.svg"></head><body class="rustdoc mod sys"><!--[if lte IE 11]><div class="warning">This old browser is unsupported and will most likely display funky things.</div><![endif]--><nav class="mobile-topbar"><button class="sidebar-menu-toggle" title="show sidebar"></button></nav><nav class="sidebar"><div class="sidebar-crate"><h2><a href="../fasten/index.html">fasten</a><span class="version">0.8.9</span></h2></div><div class="sidebar-elems"><section id="rustdoc-toc"><h3><a href="#macros">Crate Items</a></h3><ul class="block"><li><a href="#macros" title="Macros">Macros</a></li><li><a href="#structs" title="Structs">Structs</a></li><li><a href="#traits" title="Traits">Traits</a></li><li><a href="#functions" title="Functions">Functions</a></li></ul></section><div id="rustdoc-modnav"></div></div></nav><div class="sidebar-resizer"></div><main><div class="width-limiter"><rustdoc-search></rustdoc-search><section id="main-content" class="content"><h1>List of all items</h1><h3 id="structs">Structs</h3><ul class="all-items"><li><a href="io/fastq/struct.FastqReader.html">io::fastq::FastqReader</a></li><li><a href="io/seq/struct.Seq.html">io::seq::Seq</a></li></ul><h3 id="traits">Traits</h3><ul class="all-items"><li><a href="io/seq/trait.Cleanable.html">io::seq::Cleanable</a></li></ul><h3 id="macros">Macros</h3><ul class="all-items"><li><a href="macro.print.html">print</a></li></ul><h3 id="functions">Functions</h3><ul class="all-items"><li><a href="fn.eexit.html">eexit</a></li><li><a href="fn.fasten_base_options.html">fasten_base_options</a></li><li><a href="fn.fasten_base_options_matches.html">fasten_base_options_matches</a></li><li><a href="fn.logmsg.html">logmsg</a></li><li><a href="fn.reverse_complement.html">reverse_complement</a></li></ul></section></div></main></body></html>
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‎docs/fasten/fn.eexit.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="Propagate an error by printing invalid read(s)"><title>eexit in fasten - Rust</title><script>if(window.location.protocol!=="file:")document.head.insertAdjacentHTML("beforeend","SourceSerif4-Regular-46f98efaafac5295.ttf.woff2,FiraSans-Regular-018c141bf0843ffd.woff2,FiraSans-Medium-8f9a781e4970d388.woff2,SourceCodePro-Regular-562dcc5011b6de7d.ttf.woff2,SourceCodePro-Semibold-d899c5a5c4aeb14a.ttf.woff2".split(",").map(f=>`<link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/${f}">`).join(""))</script><link rel="stylesheet" href="../static.files/normalize-76eba96aa4d2e634.css"><link rel="stylesheet" href="../static.files/rustdoc-b0742ba02757f159.css"><meta name="rustdoc-vars" data-root-path="../" data-static-root-path="../static.files/" data-current-crate="fasten" data-themes="" data-resource-suffix="" data-rustdoc-version="1.83.0 (90b35a623 2024-11-26)" data-channel="1.83.0" data-search-js="search-f0d225181b97f9a4.js" data-settings-js="settings-805db61a62df4bd2.js" ><script src="../static.files/storage-1d39b6787ed640ff.js"></script><script defer src="sidebar-items.js"></script><script defer src="../static.files/main-f070b9041d14864c.js"></script><noscript><link rel="stylesheet" href="../static.files/noscript-0111fcff984fae8f.css"></noscript><link rel="alternate icon" type="image/png" href="../static.files/favicon-32x32-422f7d1d52889060.png"><link rel="icon" type="image/svg+xml" href="../static.files/favicon-2c020d218678b618.svg"></head><body class="rustdoc fn"><!--[if lte IE 11]><div class="warning">This old browser is unsupported and will most likely display funky things.</div><![endif]--><nav class="mobile-topbar"><button class="sidebar-menu-toggle" title="show sidebar"></button></nav><nav class="sidebar"><div class="sidebar-crate"><h2><a href="../fasten/index.html">fasten</a><span class="version">0.9.0</span></h2></div><div class="sidebar-elems"><div id="rustdoc-modnav"></div></div></nav><div class="sidebar-resizer"></div><main><div class="width-limiter"><rustdoc-search></rustdoc-search><section id="main-content" class="content"><div class="main-heading"><span class="rustdoc-breadcrumbs"><a href="index.html">fasten</a></span><h1>Function <span class="fn">eexit</span><button id="copy-path" title="Copy item path to clipboard">Copy item path</button></h1><rustdoc-toolbar></rustdoc-toolbar><span class="sub-heading"><a class="src" href="../src/fasten/lib.rs.html#91-94">source</a> </span></div><pre class="rust item-decl"><code>pub fn eexit()</code></pre><details class="toggle top-doc" open><summary class="hideme"><span>Expand description</span></summary><div class="docblock"><p>Propagate an error by printing invalid read(s)</p>
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‎docs/fasten/fn.fasten_base_options.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="a function that reads an options object and adds fasten default options."><title>fasten_base_options in fasten - Rust</title><script>if(window.location.protocol!=="file:")document.head.insertAdjacentHTML("beforeend","SourceSerif4-Regular-46f98efaafac5295.ttf.woff2,FiraSans-Regular-018c141bf0843ffd.woff2,FiraSans-Medium-8f9a781e4970d388.woff2,SourceCodePro-Regular-562dcc5011b6de7d.ttf.woff2,SourceCodePro-Semibold-d899c5a5c4aeb14a.ttf.woff2".split(",").map(f=>`<link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/${f}">`).join(""))</script><link rel="stylesheet" href="../static.files/normalize-76eba96aa4d2e634.css"><link rel="stylesheet" href="../static.files/rustdoc-b0742ba02757f159.css"><meta name="rustdoc-vars" data-root-path="../" data-static-root-path="../static.files/" data-current-crate="fasten" data-themes="" data-resource-suffix="" data-rustdoc-version="1.83.0 (90b35a623 2024-11-26)" data-channel="1.83.0" data-search-js="search-f0d225181b97f9a4.js" data-settings-js="settings-805db61a62df4bd2.js" ><script src="../static.files/storage-1d39b6787ed640ff.js"></script><script defer src="sidebar-items.js"></script><script defer src="../static.files/main-f070b9041d14864c.js"></script><noscript><link rel="stylesheet" href="../static.files/noscript-0111fcff984fae8f.css"></noscript><link rel="alternate icon" type="image/png" href="../static.files/favicon-32x32-422f7d1d52889060.png"><link rel="icon" type="image/svg+xml" href="../static.files/favicon-2c020d218678b618.svg"></head><body class="rustdoc fn"><!--[if lte IE 11]><div class="warning">This old browser is unsupported and will most likely display funky things.</div><![endif]--><nav class="mobile-topbar"><button class="sidebar-menu-toggle" title="show sidebar"></button></nav><nav class="sidebar"><div class="sidebar-crate"><h2><a href="../fasten/index.html">fasten</a><span class="version">0.9.0</span></h2></div><div class="sidebar-elems"><div id="rustdoc-modnav"></div></div></nav><div class="sidebar-resizer"></div><main><div class="width-limiter"><rustdoc-search></rustdoc-search><section id="main-content" class="content"><div class="main-heading"><span class="rustdoc-breadcrumbs"><a href="index.html">fasten</a></span><h1>Function <span class="fn">fasten_base_options</span><button id="copy-path" title="Copy item path to clipboard">Copy item path</button></h1><rustdoc-toolbar></rustdoc-toolbar><span class="sub-heading"><a class="src" href="../src/fasten/lib.rs.html#114-123">source</a> </span></div><pre class="rust item-decl"><code>pub fn fasten_base_options() -&gt; <a class="struct" href="https://docs.rs/getopts/0.2.20/getopts/struct.Options.html" title="struct getopts::Options">Options</a></code></pre><details class="toggle top-doc" open><summary class="hideme"><span>Expand description</span></summary><div class="docblock"><p>a function that reads an options object and adds fasten default options.</p>
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