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Fasten trim: updated documentation (#38)
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* trim-adapters

* fixed rev math

* fix fasten_trim test

* update upload-artifact

* docs

* fix up documentation a bit

* updated docs
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@lskatz
lskatz authored Jan 6, 2025
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16 changes: 8 additions & 8 deletions README.md
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Expand Up @@ -103,13 +103,13 @@ except `fasten_convert`.
|[`fasten_validate`](https://lskatz.github.io/fasten/fasten_validate) | Validates your reads (deprecated in favor of `fasten_inspect` and `fasten_repair`|
|[`fasten_inspect`](https://lskatz.github.io/fasten/fasten_inspect) | adds information to read IDs such as seqlength |
|[`fasten_repair`](https://lskatz.github.io/fasten/fasten_repair) | Repairs corrupted reads |
|[`fasten_quality_filter`](https://lskatz.github.io/fasten/fasten_quality_filter) | Transforms nucleotides to "N" if the quality is low | |
|[`fasten_trim`](https://lskatz.github.io/fasten/fasten_trim) | Blunt-end trims reads | |
|[`fasten_replace`](https://lskatz.github.io/fasten/fasten_replace) | Find and replace using regex | |
|[`fasten_mutate`](https://lskatz.github.io/fasten/fasten_mutate) | introduce random mutations | |
|[`fasten_regex`](https://lskatz.github.io/fasten/fasten_regex) | Filter for reads using regex | |
|[`fasten_progress`](https://lskatz.github.io/fasten/fasten_progress) | Add progress to any place in the pipeline | |
|[`fasten_sort`](https://lskatz.github.io/fasten/fasten_sort) | Sort fastq entries | |
|[`fasten_quality_filter`](https://lskatz.github.io/fasten/fasten_quality_filter) | Transforms nucleotides to "N" if the quality is low |
|[`fasten_trim`](https://lskatz.github.io/fasten/fasten_trim) | Blunt-end trims reads |
|[`fasten_replace`](https://lskatz.github.io/fasten/fasten_replace) | Find and replace using regex |
|[`fasten_mutate`](https://lskatz.github.io/fasten/fasten_mutate) | introduce random mutations |
|[`fasten_regex`](https://lskatz.github.io/fasten/fasten_regex) | Filter for reads using regex |
|[`fasten_progress`](https://lskatz.github.io/fasten/fasten_progress) | Add progress to any place in the pipeline |
|[`fasten_sort`](https://lskatz.github.io/fasten/fasten_sort) | Sort fastq entries |

## Etymology

Expand All @@ -121,4 +121,4 @@ that indicates that you are securing your analysis by "fasten"ing it (with a sil

[![DOI](https://joss.theoj.org/papers/10.21105/joss.06030/status.svg)](https://doi.org/10.21105/joss.06030)

To cite, please refer to Katz et al., (2024). Fasten: a toolkit for streaming operations on fastq files. Journal of Open Source Software, 9(94), 6030, https://doi.org/10.21105/joss.06030
To cite, please refer to Katz et al., (2024). Fasten: a toolkit for streaming operations on fastq files. Journal of Open Source Software, 9(94), 6030, <https://doi.org/10.21105/joss.06030>
2 changes: 1 addition & 1 deletion docs/fasten_trim/fn.main.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="API documentation for the Rust `main` fn in crate `fasten_trim`."><title>main in fasten_trim - Rust</title><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/SourceSerif4-Regular-46f98efaafac5295.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/FiraSans-Regular-018c141bf0843ffd.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/FiraSans-Medium-8f9a781e4970d388.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/SourceCodePro-Regular-562dcc5011b6de7d.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/SourceCodePro-Semibold-d899c5a5c4aeb14a.ttf.woff2"><link rel="stylesheet" href="../static.files/normalize-76eba96aa4d2e634.css"><link rel="stylesheet" href="../static.files/rustdoc-5bc39a1768837dd0.css"><meta name="rustdoc-vars" data-root-path="../" data-static-root-path="../static.files/" data-current-crate="fasten_trim" data-themes="" data-resource-suffix="" data-rustdoc-version="1.77.0 (aedd173a2 2024-03-17)" data-channel="1.77.0" data-search-js="search-dd67cee4cfa65049.js" data-settings-js="settings-4313503d2e1961c2.js" ><script src="../static.files/storage-4c98445ec4002617.js"></script><script defer src="sidebar-items.js"></script><script defer src="../static.files/main-48f368f3872407c8.js"></script><noscript><link rel="stylesheet" href="../static.files/noscript-04d5337699b92874.css"></noscript><link rel="alternate icon" type="image/png" href="../static.files/favicon-16x16-8b506e7a72182f1c.png"><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_trim/index.html">fasten_trim</a><span class="version">0.8.4</span></h2></div><div class="sidebar-elems"></div></nav><div class="sidebar-resizer"></div>
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="../fasten_trim/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="../help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Function <a href="index.html">fasten_trim</a>::<wbr><a class="fn" href="#">main</a><button id="copy-path" title="Copy item path to clipboard"><img src="../static.files/clipboard-7571035ce49a181d.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="src" href="../src/fasten_trim/fasten_trim.rs.html#92-181">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></span></div><pre class="rust item-decl"><code>pub(crate) fn main()</code></pre></section></div></main></body></html>
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="../fasten_trim/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="../help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Function <a href="index.html">fasten_trim</a>::<wbr><a class="fn" href="#">main</a><button id="copy-path" title="Copy item path to clipboard"><img src="../static.files/clipboard-7571035ce49a181d.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="src" href="../src/fasten_trim/fasten_trim.rs.html#105-194">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></span></div><pre class="rust item-decl"><code>pub(crate) fn main()</code></pre></section></div></main></body></html>
2 changes: 1 addition & 1 deletion docs/fasten_trim/fn.read_fasta.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="Read a fasta file and return a HashMap of the sequences"><title>read_fasta in fasten_trim - Rust</title><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/SourceSerif4-Regular-46f98efaafac5295.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/FiraSans-Regular-018c141bf0843ffd.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/FiraSans-Medium-8f9a781e4970d388.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/SourceCodePro-Regular-562dcc5011b6de7d.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/SourceCodePro-Semibold-d899c5a5c4aeb14a.ttf.woff2"><link rel="stylesheet" href="../static.files/normalize-76eba96aa4d2e634.css"><link rel="stylesheet" href="../static.files/rustdoc-5bc39a1768837dd0.css"><meta name="rustdoc-vars" data-root-path="../" data-static-root-path="../static.files/" data-current-crate="fasten_trim" data-themes="" data-resource-suffix="" data-rustdoc-version="1.77.0 (aedd173a2 2024-03-17)" data-channel="1.77.0" data-search-js="search-dd67cee4cfa65049.js" data-settings-js="settings-4313503d2e1961c2.js" ><script src="../static.files/storage-4c98445ec4002617.js"></script><script defer src="sidebar-items.js"></script><script defer src="../static.files/main-48f368f3872407c8.js"></script><noscript><link rel="stylesheet" href="../static.files/noscript-04d5337699b92874.css"></noscript><link rel="alternate icon" type="image/png" href="../static.files/favicon-16x16-8b506e7a72182f1c.png"><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_trim/index.html">fasten_trim</a><span class="version">0.8.4</span></h2></div><div class="sidebar-elems"></div></nav><div class="sidebar-resizer"></div>
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="../fasten_trim/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="../help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Function <a href="index.html">fasten_trim</a>::<wbr><a class="fn" href="#">read_fasta</a><button id="copy-path" title="Copy item path to clipboard"><img src="../static.files/clipboard-7571035ce49a181d.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="src" href="../src/fasten_trim/fasten_trim.rs.html#258-280">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></span></div><pre class="rust item-decl"><code>pub(crate) fn read_fasta(file_path: &amp;<a class="primitive" href="https://doc.rust-lang.org/1.77.0/std/primitive.str.html">str</a>) -&gt; <a class="struct" href="https://doc.rust-lang.org/1.77.0/std/collections/hash/map/struct.HashMap.html" title="struct std::collections::hash::map::HashMap">HashMap</a>&lt;<a class="struct" href="https://doc.rust-lang.org/1.77.0/alloc/string/struct.String.html" title="struct alloc::string::String">String</a>, <a class="struct" href="https://doc.rust-lang.org/1.77.0/alloc/string/struct.String.html" title="struct alloc::string::String">String</a>&gt;</code></pre><details class="toggle top-doc" open><summary class="hideme"><span>Expand description</span></summary><div class="docblock"><p>Read a fasta file and return a HashMap of the sequences</p>
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="../fasten_trim/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="../help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Function <a href="index.html">fasten_trim</a>::<wbr><a class="fn" href="#">read_fasta</a><button id="copy-path" title="Copy item path to clipboard"><img src="../static.files/clipboard-7571035ce49a181d.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="src" href="../src/fasten_trim/fasten_trim.rs.html#271-293">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></span></div><pre class="rust item-decl"><code>pub(crate) fn read_fasta(file_path: &amp;<a class="primitive" href="https://doc.rust-lang.org/1.77.0/std/primitive.str.html">str</a>) -&gt; <a class="struct" href="https://doc.rust-lang.org/1.77.0/std/collections/hash/map/struct.HashMap.html" title="struct std::collections::hash::map::HashMap">HashMap</a>&lt;<a class="struct" href="https://doc.rust-lang.org/1.77.0/alloc/string/struct.String.html" title="struct alloc::string::String">String</a>, <a class="struct" href="https://doc.rust-lang.org/1.77.0/alloc/string/struct.String.html" title="struct alloc::string::String">String</a>&gt;</code></pre><details class="toggle top-doc" open><summary class="hideme"><span>Expand description</span></summary><div class="docblock"><p>Read a fasta file and return a HashMap of the sequences</p>
</div></details></section></div></main></body></html>
2 changes: 1 addition & 1 deletion docs/fasten_trim/fn.trim_worker.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="Trim a set of fastq entries and send it to a channel"><title>trim_worker in fasten_trim - Rust</title><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/SourceSerif4-Regular-46f98efaafac5295.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/FiraSans-Regular-018c141bf0843ffd.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/FiraSans-Medium-8f9a781e4970d388.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/SourceCodePro-Regular-562dcc5011b6de7d.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../static.files/SourceCodePro-Semibold-d899c5a5c4aeb14a.ttf.woff2"><link rel="stylesheet" href="../static.files/normalize-76eba96aa4d2e634.css"><link rel="stylesheet" href="../static.files/rustdoc-5bc39a1768837dd0.css"><meta name="rustdoc-vars" data-root-path="../" data-static-root-path="../static.files/" data-current-crate="fasten_trim" data-themes="" data-resource-suffix="" data-rustdoc-version="1.77.0 (aedd173a2 2024-03-17)" data-channel="1.77.0" data-search-js="search-dd67cee4cfa65049.js" data-settings-js="settings-4313503d2e1961c2.js" ><script src="../static.files/storage-4c98445ec4002617.js"></script><script defer src="sidebar-items.js"></script><script defer src="../static.files/main-48f368f3872407c8.js"></script><noscript><link rel="stylesheet" href="../static.files/noscript-04d5337699b92874.css"></noscript><link rel="alternate icon" type="image/png" href="../static.files/favicon-16x16-8b506e7a72182f1c.png"><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_trim/index.html">fasten_trim</a><span class="version">0.8.4</span></h2></div><div class="sidebar-elems"></div></nav><div class="sidebar-resizer"></div>
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="../fasten_trim/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="../help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Function <a href="index.html">fasten_trim</a>::<wbr><a class="fn" href="#">trim_worker</a><button id="copy-path" title="Copy item path to clipboard"><img src="../static.files/clipboard-7571035ce49a181d.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="src" href="../src/fasten_trim/fasten_trim.rs.html#184-254">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></span></div><pre class="rust item-decl"><code>pub(crate) fn trim_worker(
<main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><div id="sidebar-button" tabindex="-1"><a href="../fasten_trim/all.html" title="show sidebar"></a></div><input class="search-input" name="search" aria-label="Run search in the documentation" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" tabindex="-1"><a href="../help.html" title="help">?</a></div><div id="settings-menu" tabindex="-1"><a href="../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../static.files/wheel-7b819b6101059cd0.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1>Function <a href="index.html">fasten_trim</a>::<wbr><a class="fn" href="#">trim_worker</a><button id="copy-path" title="Copy item path to clipboard"><img src="../static.files/clipboard-7571035ce49a181d.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="src" href="../src/fasten_trim/fasten_trim.rs.html#197-267">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></span></div><pre class="rust item-decl"><code>pub(crate) fn trim_worker(
seq: <a class="struct" href="../fasten/io/seq/struct.Seq.html" title="struct fasten::io::seq::Seq">Seq</a>,
suggested_first_base: <a class="primitive" href="https://doc.rust-lang.org/1.77.0/std/primitive.usize.html">usize</a>,
suggested_last_base: <a class="primitive" href="https://doc.rust-lang.org/1.77.0/std/primitive.usize.html">usize</a>,
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