Merge pull request #7 from MPI-EVA-Archaeogenetics/pmmread

Add toolbox pmrread
MPI-EVA-Archaeogenetics · Mar 11, 2024 · f79a625 · f79a625
2 parents 4532a41 + e7d8b9a
commit f79a625
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Showing 69 changed files with 17,904 additions and 687 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/_quarto.yml b/_quarto.yml
@@ -13,6 +13,7 @@ book:
     - fstats.qmd
     - eager.qmd
     - fst.qmd
+    - pmrread.qmd
     - references.qmd
 
 bibliography: references.bib

diff --git a/docs/Quarto_intro.html b/docs/Quarto_intro.html
diff --git a/docs/eager.html b/docs/eager.html
diff --git a/docs/fst.html b/docs/fst.html
diff --git a/docs/fstats.html b/docs/fstats.html
diff --git a/docs/img/pmrread/Alacamli.F5.Folwchart.jpg b/docs/img/pmrread/Alacamli.F5.Folwchart.jpg
diff --git a/docs/img/pmrread/Alacamli.TS1.gif b/docs/img/pmrread/Alacamli.TS1.gif
diff --git a/docs/img/pmrread/CoefficientsOfRelatednessAndKinship.JPG b/docs/img/pmrread/CoefficientsOfRelatednessAndKinship.JPG
diff --git a/docs/img/pmrread/PMRcalculation.jpg b/docs/img/pmrread/PMRcalculation.jpg
diff --git a/docs/img/pmrread/READ1.JPG b/docs/img/pmrread/READ1.JPG
diff --git a/docs/img/pmrread/READ_results_plot.jpg b/docs/img/pmrread/READ_results_plot.jpg
diff --git a/docs/img/pmrread/READv2_result_plot.jpg b/docs/img/pmrread/READv2_result_plot.jpg
diff --git a/docs/index.html b/docs/index.html
@@ -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-1.1.163">
+<meta name="generator" content="quarto-1.3.450">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -19,7 +19,7 @@
 ul.task-list{list-style: none;}
 ul.task-list li input[type="checkbox"] {
   width: 0.8em;
-  margin: 0 0.8em 0.2em -1.6em;
+  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
   vertical-align: middle;
 }
 </style>
@@ -58,7 +58,8 @@
     "search-more-matches-text": "more matches in this document",
     "search-clear-button-title": "Clear",
     "search-detached-cancel-button-title": "Cancel",
-    "search-submit-button-title": "Submit"
+    "search-submit-button-title": "Submit",
+    "search-label": "Search"
   }
 }</script>
 
@@ -69,69 +70,88 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-  <nav class="quarto-secondary-nav" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
-    <div class="container-fluid d-flex justify-content-between">
-      <h1 class="quarto-secondary-nav-title">Computational Methods for human population genetics and ancient DNA</h1>
-      <button type="button" class="quarto-btn-toggle btn" aria-label="Show secondary navigation">
-        <i class="bi bi-chevron-right"></i>
+  <nav class="quarto-secondary-nav">
+    <div class="container-fluid d-flex">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+        <i class="bi bi-layout-text-sidebar-reverse"></i>
+      </button>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html">Preface</a></li></ol></nav>
+      <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+      </a>
+      <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
+        <i class="bi bi-search"></i>
       </button>
     </div>
   </nav>
 </header>
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse sidebar-navigation floating overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
     <div class="pt-lg-2 mt-2 text-left sidebar-header">
     <div class="sidebar-title mb-0 py-0">
       <a href="./">Computational Methods for human population genetics and ancient DNA</a> 
     </div>
       </div>
-      <div class="mt-2 flex-shrink-0 align-items-center">
+        <div class="mt-2 flex-shrink-0 align-items-center">
         <div class="sidebar-search">
         <div id="quarto-search" class="" title="Search"></div>
         </div>
-      </div>
+        </div>
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./index.html" class="sidebar-item-text sidebar-link active">Preface</a>
+  <a href="./index.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text">Preface</span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./Quarto_intro.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction to Quarto</span></a>
+  <a href="./Quarto_intro.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction to Quarto</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./poseidon.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Genotype and context data management with Poseidon</span></a>
+  <a href="./poseidon.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Genotype and context data management with Poseidon</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./fstats.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Introduction to F3- and F4-Statistics</span></a>
+  <a href="./fstats.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Introduction to F3- and F4-Statistics</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./eager.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Introduction to nf-core/eager</span></a>
+  <a href="./eager.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Introduction to nf-core/eager</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./fst.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Measuring population structure using Fst</span></a>
+  <a href="./fst.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Measuring population structure using Fst</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./references.html" class="sidebar-item-text sidebar-link">References</a>
+  <a href="./pmrread.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Pairwise mismatch rate (PMR) and READ relatedness inference</span></span></a>
+  </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./references.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">References</span></a>
   </div>
 </li>
     </ul>
     </div>
 </nav>
+<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active">
@@ -147,7 +167,7 @@ <h2 id="toc-title">Table of contents</h2>
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title d-none d-lg-block">Computational Methods for human population genetics and ancient DNA</h1>
+<h1 class="title">Computational Methods for human population genetics and ancient DNA</h1>
 </div>
 
 
@@ -167,6 +187,7 @@ <h1 class="title d-none d-lg-block">Computational Methods for human population g
       <p class="date">September 21, 2023</p>
     </div>
   </div>
+
 
   </div>
 
@@ -209,9 +230,23 @@ <h1 class="unnumbered">Preface</h1>
     icon: icon
   };
   anchorJS.add('.anchored');
+  const isCodeAnnotation = (el) => {
+    for (const clz of el.classList) {
+      if (clz.startsWith('code-annotation-')) {                     
+        return true;
+      }
+    }
+    return false;
+  }
   const clipboard = new window.ClipboardJS('.code-copy-button', {
-    target: function(trigger) {
-      return trigger.previousElementSibling;
+    text: function(trigger) {
+      const codeEl = trigger.previousElementSibling.cloneNode(true);
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
     }
   });
   clipboard.on('success', function(e) {
@@ -223,7 +258,24 @@ <h1 class="unnumbered">Preface</h1>
     button.classList.add('code-copy-button-checked');
     var currentTitle = button.getAttribute("title");
     button.setAttribute("title", "Copied!");
+    let tooltip;
+    if (window.bootstrap) {
+      button.setAttribute("data-bs-toggle", "tooltip");
+      button.setAttribute("data-bs-placement", "left");
+      button.setAttribute("data-bs-title", "Copied!");
+      tooltip = new bootstrap.Tooltip(button, 
+        { trigger: "manual", 
+          customClass: "code-copy-button-tooltip",
+          offset: [0, -8]});
+      tooltip.show();    
+    }
     setTimeout(function() {
+      if (tooltip) {
+        tooltip.hide();
+        button.removeAttribute("data-bs-title");
+        button.removeAttribute("data-bs-toggle");
+        button.removeAttribute("data-bs-placement");
+      }
       button.setAttribute("title", currentTitle);
       button.classList.remove('code-copy-button-checked');
     }, 1000);
@@ -259,24 +311,128 @@ <h1 class="unnumbered">Preface</h1>
       return note.innerHTML;
     });
   }
+      let selectedAnnoteEl;
+      const selectorForAnnotation = ( cell, annotation) => {
+        let cellAttr = 'data-code-cell="' + cell + '"';
+        let lineAttr = 'data-code-annotation="' +  annotation + '"';
+        const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
+        return selector;
+      }
+      const selectCodeLines = (annoteEl) => {
+        const doc = window.document;
+        const targetCell = annoteEl.getAttribute("data-target-cell");
+        const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
+        const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
+        const lines = annoteSpan.getAttribute("data-code-lines").split(",");
+        const lineIds = lines.map((line) => {
+          return targetCell + "-" + line;
+        })
+        let top = null;
+        let height = null;
+        let parent = null;
+        if (lineIds.length > 0) {
+            //compute the position of the single el (top and bottom and make a div)
+            const el = window.document.getElementById(lineIds[0]);
+            top = el.offsetTop;
+            height = el.offsetHeight;
+            parent = el.parentElement.parentElement;
+          if (lineIds.length > 1) {
+            const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
+            const bottom = lastEl.offsetTop + lastEl.offsetHeight;
+            height = bottom - top;
+          }
+          if (top !== null && height !== null && parent !== null) {
+            // cook up a div (if necessary) and position it 
+            let div = window.document.getElementById("code-annotation-line-highlight");
+            if (div === null) {
+              div = window.document.createElement("div");
+              div.setAttribute("id", "code-annotation-line-highlight");
+              div.style.position = 'absolute';
+              parent.appendChild(div);
+            }
+            div.style.top = top - 2 + "px";
+            div.style.height = height + 4 + "px";
+            let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
+            if (gutterDiv === null) {
+              gutterDiv = window.document.createElement("div");
+              gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
+              gutterDiv.style.position = 'absolute';
+              const codeCell = window.document.getElementById(targetCell);
+              const gutter = codeCell.querySelector('.code-annotation-gutter');
+              gutter.appendChild(gutterDiv);
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+            gutterDiv.style.top = top - 2 + "px";
+            gutterDiv.style.height = height + 4 + "px";
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+          selectedAnnoteEl = annoteEl;
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+      const unselectCodeLines = () => {
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+          if (div) {
+            div.remove();
+          }
+        });
+        selectedAnnoteEl = undefined;
+      };
+      // Attach click handler to the DT
+      const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
+      for (const annoteDlNode of annoteDls) {
+        annoteDlNode.addEventListener('click', (event) => {
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+          if (clickedEl !== selectedAnnoteEl) {
+            unselectCodeLines();
+            const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
+            if (activeEl) {
+              activeEl.classList.remove('code-annotation-active');
+            }
+            selectCodeLines(clickedEl);
+            clickedEl.classList.add('code-annotation-active');
+          } else {
+            // Unselect the line
+            unselectCodeLines();
+            clickedEl.classList.remove('code-annotation-active');
+          }
+        });
+      }
+  const findCites = (el) => {
+    const parentEl = el.parentElement;
+    if (parentEl) {
+      const cites = parentEl.dataset.cites;
+      if (cites) {
+        return {
+          el,
+          cites: cites.split(' ')
+        };
+      } else {
+        return findCites(el.parentElement)
+      }
+    } else {
+      return undefined;
+    }
+  };
   var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
   for (var i=0; i<bibliorefs.length; i++) {
     const ref = bibliorefs[i];
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-    tippyHover(ref, function() {
-      var popup = window.document.createElement('div');
-      cites.forEach(function(cite) {
-        var citeDiv = window.document.createElement('div');
-        citeDiv.classList.add('hanging-indent');
-        citeDiv.classList.add('csl-entry');
-        var biblioDiv = window.document.getElementById('ref-' + cite);
-        if (biblioDiv) {
-          citeDiv.innerHTML = biblioDiv.innerHTML;
-        }
-        popup.appendChild(citeDiv);
+    const citeInfo = findCites(ref);
+    if (citeInfo) {
+      tippyHover(citeInfo.el, function() {
+        var popup = window.document.createElement('div');
+        citeInfo.cites.forEach(function(cite) {
+          var citeDiv = window.document.createElement('div');
+          citeDiv.classList.add('hanging-indent');
+          citeDiv.classList.add('csl-entry');
+          var biblioDiv = window.document.getElementById('ref-' + cite);
+          if (biblioDiv) {
+            citeDiv.innerHTML = biblioDiv.innerHTML;
+          }
+          popup.appendChild(citeDiv);
+        });
+        return popup.innerHTML;
       });
-      return popup.innerHTML;
-    });
+    }
   }
 });
 </script>