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Fasten trim: add adapter trimming #37

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Jan 6, 2025
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Fasten trim: add adapter trimming #37

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c1a5905
trim-adapters
lskatz Jan 4, 2025
f9d9a94
fixed rev math
lskatz Jan 4, 2025
c947bd7
fix fasten_trim test
lskatz Jan 4, 2025
448fddd
update upload-artifact
lskatz Jan 4, 2025
3d2f964
docs
lskatz Jan 4, 2025
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4 changes: 2 additions & 2 deletions .github/workflows/draft-pdf.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
tree
find . -type f -name '*immem*'
- name: Upload
uses: actions/upload-artifact@v1
uses: actions/upload-artifact@v4
with:
name: immem-abstract
# This is the output path where Pandoc will write the compiled
Expand All @@ -43,7 +43,7 @@ jobs:
tree
find . -type f -name '*paper*'
- name: Upload
uses: actions/upload-artifact@v1
uses: actions/upload-artifact@v4
with:
name: paper-abstract
# This is the output path where Pandoc will write the compiled
Expand Down
3 changes: 2 additions & 1 deletion Cargo.toml
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@@ -1,6 +1,6 @@
[package]
name = "fasten"
version = "0.8.3"
version = "0.8.4"
authors = ["Lee Katz <[email protected]>"]
#license-file = "LICENSE"
license = "MIT"
Expand Down Expand Up @@ -104,6 +104,7 @@ path = "src/bin/fasten_normalize.rs"

[dependencies]
regex = "1.10"
fancy-regex = "0.13"
getopts = "0.2.21"
statistical = "1.0"
multiqueue = "0.3.2"
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3 changes: 2 additions & 1 deletion docs/fasten/all.html
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@@ -1 +1,2 @@
<!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><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/SourceSerif4-Bold-a2c9cd1067f8b328.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-cb6f1f67f1bcd037.css" id="mainThemeStyle"><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="1.73.0 (cc66ad468 2023-10-03)" data-channel="1.73.0" data-search-js="search-6dfdfced5eff6596.js" data-settings-js="settings-de11bff964e9d4e5.js" data-settings-css="settings-8c76f75bfb6bd192.css" data-theme-light-css="light-1596385f77d47ef2.css" data-theme-dark-css="dark-0a43001d3fc2282c.css" data-theme-ayu-css="ayu-fd19013d6ce078bf.css" ><script src="../static.files/storage-db41da1a38ea3cb8.js"></script><script defer src="../static.files/main-0795b7d26be81095.js"></script><noscript><link rel="stylesheet" media="(prefers-color-scheme:light)" href="../static.files/light-1596385f77d47ef2.css"><link rel="stylesheet" media="(prefers-color-scheme:dark)" href="../static.files/dark-0a43001d3fc2282c.css"><link rel="stylesheet" href="../static.files/noscript-cffde32267a19fd6.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 mod"><!--[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">&#9776;</button><a class="logo-container" href="../fasten/index.html"><img class="rust-logo" src="../static.files/rust-logo-151179464ae7ed46.svg" alt="logo"></a><h2></h2></nav><nav class="sidebar"><a class="logo-container" href="../fasten/index.html"><img class="rust-logo" src="../static.files/rust-logo-151179464ae7ed46.svg" alt="logo"></a><h2 class="location"><a href="#">Crate fasten</a></h2><div class="sidebar-elems"><section><ul class="block"><li><a href="#macros">Macros</a></li><li><a href="#structs">Structs</a></li><li><a href="#traits">Traits</a></li><li><a href="#functions">Functions</a></li></ul></section></div></nav><main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><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" title="help" tabindex="-1"><a href="../help.html">?</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"><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></ul></section></div></main></body></html>
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3 changes: 2 additions & 1 deletion 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><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/SourceSerif4-Bold-a2c9cd1067f8b328.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-cb6f1f67f1bcd037.css" id="mainThemeStyle"><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="1.73.0 (cc66ad468 2023-10-03)" data-channel="1.73.0" data-search-js="search-6dfdfced5eff6596.js" data-settings-js="settings-de11bff964e9d4e5.js" data-settings-css="settings-8c76f75bfb6bd192.css" data-theme-light-css="light-1596385f77d47ef2.css" data-theme-dark-css="dark-0a43001d3fc2282c.css" data-theme-ayu-css="ayu-fd19013d6ce078bf.css" ><script src="../static.files/storage-db41da1a38ea3cb8.js"></script><script defer src="sidebar-items.js"></script><script defer src="../static.files/main-0795b7d26be81095.js"></script><noscript><link rel="stylesheet" media="(prefers-color-scheme:light)" href="../static.files/light-1596385f77d47ef2.css"><link rel="stylesheet" media="(prefers-color-scheme:dark)" href="../static.files/dark-0a43001d3fc2282c.css"><link rel="stylesheet" href="../static.files/noscript-cffde32267a19fd6.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">&#9776;</button><a class="logo-container" href="../fasten/index.html"><img class="rust-logo" src="../static.files/rust-logo-151179464ae7ed46.svg" alt="logo"></a><h2></h2></nav><nav class="sidebar"><a class="logo-container" href="../fasten/index.html"><img class="rust-logo" src="../static.files/rust-logo-151179464ae7ed46.svg" alt="logo"></a><div class="sidebar-elems"><h2><a href="index.html">In fasten</a></h2></div></nav><main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><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" title="help" tabindex="-1"><a href="../help.html">?</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</a>::<wbr><a class="fn" href="#">eexit</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/lib.rs.html#90-93">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></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>
<!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><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" 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/index.html">fasten</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/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</a>::<wbr><a class="fn" href="#">eexit</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/lib.rs.html#91-94">source</a> · <button id="toggle-all-docs" title="collapse all docs">[<span>&#x2212;</span>]</button></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>
</div></details></section></div></main></body></html>
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