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Quarto GHA Workflow Runner committed Mar 6, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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4a188cda
30cc38f6
26 changes: 24 additions & 2 deletions 404.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.550">
<meta name="generator" content="quarto-1.4.551">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -274,6 +274,24 @@ <h1 class="title">Page Not Found</h1>
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/huishenlab\.github\.io\/dupsifter\/");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -308,7 +326,11 @@ <h1 class="title">Page Not Found</h1>
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
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26 changes: 24 additions & 2 deletions examples.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.550">
<meta name="generator" content="quarto-1.4.551">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -603,6 +603,24 @@ <h3 class="anchored" data-anchor-id="gembs">gemBS</h3>
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/huishenlab\.github\.io\/dupsifter\/");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -637,7 +655,11 @@ <h3 class="anchored" data-anchor-id="gembs">gemBS</h3>
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
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26 changes: 24 additions & 2 deletions index.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.550">
<meta name="generator" content="quarto-1.4.551">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -333,6 +333,24 @@ <h2 class="anchored" data-anchor-id="acknowledgments">Acknowledgments</h2>
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/huishenlab\.github\.io\/dupsifter\/");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -367,7 +385,11 @@ <h2 class="anchored" data-anchor-id="acknowledgments">Acknowledgments</h2>
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
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58 changes: 45 additions & 13 deletions install.html
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Expand Up @@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.550">
<meta name="generator" content="quarto-1.4.551">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -237,7 +237,19 @@ <h1 class="title">Installation</h1>

<section id="external-dependencies" class="level2">
<h2 class="anchored" data-anchor-id="external-dependencies">External Dependencies</h2>
<p>Note, if you plan to use the Docker container or install via <code>conda</code>/<code>mamba</code> you can skip this section as all dependencies are wrapped up in these methods.</p>
<div class="callout callout-style-default callout-note callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
Note
</div>
</div>
<div class="callout-body-container callout-body">
<p>If you plan to use the <a href="#containers">Docker container</a> or install via <a href="#bioconda"><code>conda</code>/<code>mamba</code></a> you can skip this section as all dependencies are wrapped up in these methods.</p>
</div>
</div>
<p>If you plan to compile your own copy of <code>dupsifter</code> or run the pre-compiled binaries, there are several external dependencies that are needed:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode default code-with-copy"><code class="sourceCode default"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>zlib</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>libbz2</span>
Expand All @@ -258,16 +270,14 @@ <h2 class="anchored" data-anchor-id="download-and-install">Download and Install<
<h3 class="anchored" data-anchor-id="precompiled-binaries">Precompiled Binaries</h3>
<p>Precompiled binaries are available for macOS and Linux:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="co"># macOS</span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-OL</span> <span class="va">$(</span><span class="ex">curl</span> <span class="at">-s</span> https://api.github.com/repos/huishenlab/dupsifter/releases/latest <span class="kw">|</span></span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">grep</span> browser_download_url <span class="kw">|</span> <span class="fu">grep</span> darwin_amd64 <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-d</span> <span class="st">'"'</span> <span class="at">-f</span> 4<span class="va">)</span></span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="fu">mv</span> dupsifter_<span class="pp">*</span> dupsifter</span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a><span class="fu">chmod</span> +x dupsifter</span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a><span class="co"># Linux</span></span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-OL</span> <span class="va">$(</span><span class="ex">curl</span> <span class="at">-s</span> https://api.github.com/repos/huishenlab/dupsifter/releases/latest <span class="kw">|</span></span>
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">grep</span> browser_download_url <span class="kw">|</span> <span class="fu">grep</span> linux_amd64 <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-d</span> <span class="st">'"'</span> <span class="at">-f</span> 4<span class="va">)</span></span>
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a><span class="fu">mv</span> dupsifter_<span class="pp">*</span> dupsifter</span>
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a><span class="fu">chmod</span> +x dupsifter</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-L</span> <span class="va">$(</span><span class="ex">curl</span> <span class="at">-s</span> https://api.github.com/repos/huishenlab/dupsifter/releases/latest <span class="kw">|</span></span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">grep</span> browser_download_url <span class="kw">|</span> <span class="fu">grep</span> darwin_amd64 <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-d</span> <span class="st">'"'</span> <span class="at">-f</span> 4<span class="va">)</span> <span class="at">--output</span> dupsifter</span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="fu">chmod</span> +x dupsifter</span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a><span class="co"># Linux</span></span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-L</span> <span class="va">$(</span><span class="ex">curl</span> <span class="at">-s</span> https://api.github.com/repos/huishenlab/dupsifter/releases/latest <span class="kw">|</span></span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">grep</span> browser_download_url <span class="kw">|</span> <span class="fu">grep</span> linux_amd64 <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-d</span> <span class="st">'"'</span> <span class="at">-f</span> 4<span class="va">)</span> <span class="at">--output</span> dupsifter</span>
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a><span class="fu">chmod</span> +x dupsifter</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="build-from-source" class="level3">
<h3 class="anchored" data-anchor-id="build-from-source">Build from Source</h3>
Expand Down Expand Up @@ -397,6 +407,24 @@ <h3 class="anchored" data-anchor-id="bioconda">Bioconda</h3>
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/huishenlab\.github\.io\/dupsifter\/");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -431,7 +459,11 @@ <h3 class="anchored" data-anchor-id="bioconda">Bioconda</h3>
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
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26 changes: 24 additions & 2 deletions methodology.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.550">
<meta name="generator" content="quarto-1.4.551">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -362,6 +362,24 @@ <h2 class="anchored" data-anchor-id="bisulfite-strand-determination">Bisulfite S
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/huishenlab\.github\.io\/dupsifter\/");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -396,7 +414,11 @@ <h2 class="anchored" data-anchor-id="bisulfite-strand-determination">Bisulfite S
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
Expand Down
26 changes: 24 additions & 2 deletions releases.html
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.550">
<meta name="generator" content="quarto-1.4.551">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -318,6 +318,24 @@ <h3 class="anchored" data-anchor-id="version-1.0.0">Version 1.0.0</h3>
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/huishenlab\.github\.io\/dupsifter\/");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -352,7 +370,11 @@ <h3 class="anchored" data-anchor-id="version-1.0.0">Version 1.0.0</h3>
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
Expand Down
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