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SAM_FLAG.html
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<!DOCTYPE html>
<html lang="en">
<!-- Head tag -->
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="google-site-verification" content="xBT4GhYoi5qRD5tr338pgPM5OWHHIDR6mNg1a3euekI" />
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Chunfu的博客 | Chunfu的生信、统计知识笔记
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<a class="navbar-brand" href="/">Chunfu Shawn's Blog</a>
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<script>
// Drop Bootstarp low-performance Navbar
// Use customize navbar with high-quality material design animation
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var $body = document.body;
var $toggle = document.querySelector('.navbar-toggle');
var $navbar = document.querySelector('#huxblog_navbar');
var $collapse = document.querySelector('.navbar-collapse');
$toggle.addEventListener('click', handleMagic)
function handleMagic(e){
if ($navbar.className.indexOf('in') > 0) {
// CLOSE
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// wait until animation end.
setTimeout(function(){
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if($navbar.className.indexOf('in') < 0) {
$collapse.style.height = "0px"
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}
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<title>Explain SAM Flags</title>
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<a class="navbar-brand" href="/">SAM FLAG Tool</a>
</div>
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<nav>'s height woule be hold on by its content.
so, when navbar scale out, the <nav> will cover tags.
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<br>
This utility explains SAM flags in plain English. <br>
<br>
<form onsubmit="explainFlags(); return false;">
Flag:
<input id="tb" type="text" size="10">
<input type="submit" value="Explain"><br>
<br>
Explanation:<br>
<script type="text/javascript">
for(var i = 0; i < lstFlags.length; i++) {
document.write("<input type=checkbox name=cb" + i + " id='cb" + i + "' onclick='checkboxClicked();'> " +lstFlags[i][0] + "</input><br>");
}
</script><input type="checkbox" name="cb0" id="cb0" onclick="checkboxClicked();"> read paired<br><input type="checkbox" name="cb1" id="cb1" onclick="checkboxClicked();"> read mapped in proper pair<br><input type="checkbox" name="cb2" id="cb2" onclick="checkboxClicked();"> read unmapped<br><input type="checkbox" name="cb3" id="cb3" onclick="checkboxClicked();"> mate unmapped<br><input type="checkbox" name="cb4" id="cb4" onclick="checkboxClicked();"> read reverse strand<br><input type="checkbox" name="cb5" id="cb5" onclick="checkboxClicked();"> mate reverse strand<br><input type="checkbox" name="cb6" id="cb6" onclick="checkboxClicked();"> first in pair<br><input type="checkbox" name="cb7" id="cb7" onclick="checkboxClicked();"> second in pair<br><input type="checkbox" name="cb8" id="cb8" onclick="checkboxClicked();"> not primary alignment<br><input type="checkbox" name="cb9" id="cb9" onclick="checkboxClicked();"> read fails platform/vendor quality checks<br><input type="checkbox" name="cb10" id="cb10" onclick="checkboxClicked();"> read is PCR or optical duplicate<br>
<br>
Summary:<br>
<div id="summary">
</div>
</form>
</body>
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<script type="text/javascript">
lstFlags = [["read paired", 0x1],
["read mapped in proper pair", 0x2],
["read unmapped", 0x4],
["mate unmapped", 0x8],
["read reverse strand", 0x10],
["mate reverse strand", 0x20],
["first in pair", 0x40],
["second in pair", 0x80],
["not primary alignment", 0x100],
["read fails platform/vendor quality checks", 0x200],
["read is PCR or optical duplicate", 0x400]];
function explainFlags() {
var flagValue = parseInt(document.getElementById('tb').value); //returns 0 or NaN if can't parse
var summary = "";
for(var i = 0; i < lstFlags.length; i++) {
var checkbox = document.getElementById('cb' + i)
if(lstFlags[i][1] & flagValue) {
summary += " " + lstFlags[i][0] + "<br>";
checkbox.checked = true;
} else {
checkbox.checked = false;
}
}
document.getElementById('summary').innerHTML = summary;
}
function checkboxClicked() {
//compute the new flag value
var newFlagValue = 0;
for(var i = 0; i < lstFlags.length; i++) {
var checkBox = document.getElementById('cb' + i);
if(checkBox.checked) {
newFlagValue |= lstFlags[i][1];
}
}
var textbox = document.getElementById('tb');
textbox.value = newFlagValue;
explainFlags();
}
</script>
</html>
<!-- 如果开启评论功能 -->
<hr>
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<script type="text/javascript">
/* * * CONFIGURATION VARIABLES * * */
var disqus_shortname = "chunfushawn";
var disqus_identifier = "https://www.chunfu.site/SAM_FLAG.html";
var disqus_url = "https://www.chunfu.site/SAM_FLAG.html";
(function() {
var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js';
(document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
})();
</script>
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</div>
<!-- Sidebar Container -->
<div class="
col-lg-3 col-lg-offset-0
col-md-3 col-md-offset-0
col-sm-12
col-xs-12
sidebar-container
">
<!-- Featured Tags -->
<section>
<!-- no hr -->
<h5><a href="/tags/">FEATURED TAGS</a></h5>
<div class="tags">
<a href="/tags/#Bioinformatics" title="Bioinformatics" rel="5">Bioinformatics</a>
<a href="/tags/#Next Generation Sequencing" title="Next Generation Sequencing" rel="4">Next Generation Sequencing</a>
<a href="/tags/#Data format" title="Data format" rel="2">Data format</a>
<a href="/tags/#ATAC-seq" title="ATAC-seq" rel="1">ATAC-seq</a>
<a href="/tags/#Biology" title="Biology" rel="2">Biology</a>
<a href="/tags/#Epigenomics" title="Epigenomics" rel="1">Epigenomics</a>
<a href="/tags/#6mA" title="6mA" rel="1">6mA</a>
<a href="/tags/#Programming" title="Programming" rel="3">Programming</a>
<a href="/tags/#JavaScript" title="JavaScript" rel="3">JavaScript</a>
<a href="/tags/#R" title="R" rel="3">R</a>
<a href="/tags/#Non-parametric test" title="Non-parametric test" rel="3">Non-parametric test</a>
<a href="/tags/#Correlation" title="Correlation" rel="1">Correlation</a>
<a href="/tags/#Brain science" title="Brain science" rel="1">Brain science</a>
<a href="/tags/#Neuron" title="Neuron" rel="1">Neuron</a>
<a href="/tags/#Cerebral cortex" title="Cerebral cortex" rel="1">Cerebral cortex</a>
<a href="/tags/#Development" title="Development" rel="1">Development</a>
<a href="/tags/#Similarity Measurement" title="Similarity Measurement" rel="1">Similarity Measurement</a>
<a href="/tags/#Bash" title="Bash" rel="1">Bash</a>
<a href="/tags/#Python" title="Python" rel="1">Python</a>
<a href="/tags/#Blog" title="Blog" rel="4">Blog</a>
<a href="/tags/#Github Pages" title="Github Pages" rel="2">Github Pages</a>
<a href="/tags/#Hexo" title="Hexo" rel="2">Hexo</a>
<a href="/tags/#Data Structure" title="Data Structure" rel="2">Data Structure</a>
<a href="/tags/#Computing Methods" title="Computing Methods" rel="1">Computing Methods</a>
<a href="/tags/#Optimization" title="Optimization" rel="2">Optimization</a>
<a href="/tags/#Statistics" title="Statistics" rel="13">Statistics</a>
<a href="/tags/#Graphics" title="Graphics" rel="1">Graphics</a>
<a href="/tags/#Algorithm" title="Algorithm" rel="2">Algorithm</a>
<a href="/tags/#Hush Table" title="Hush Table" rel="1">Hush Table</a>
<a href="/tags/#Sparse Matrix" title="Sparse Matrix" rel="1">Sparse Matrix</a>
<a href="/tags/#Hypothesis test" title="Hypothesis test" rel="3">Hypothesis test</a>
<a href="/tags/#Parametric test" title="Parametric test" rel="1">Parametric test</a>
<a href="/tags/#Non-parametric estimation" title="Non-parametric estimation" rel="1">Non-parametric estimation</a>
<a href="/tags/#Mixture model" title="Mixture model" rel="2">Mixture model</a>
<a href="/tags/#Partial Observations" title="Partial Observations" rel="2">Partial Observations</a>
<a href="/tags/#Expectation-Maximization" title="Expectation-Maximization" rel="2">Expectation-Maximization</a>
<a href="/tags/#Machine Learning" title="Machine Learning" rel="2">Machine Learning</a>
<a href="/tags/#Bioinfomatics" title="Bioinfomatics" rel="1">Bioinfomatics</a>
</div>
</section>
<!-- Short About -->
<section class="visible-md visible-lg">
<hr><h5><a href="/about/">ABOUT ME</a></h5>
<div class="short-about">
<img src="/img/portrait.jpg" />
<p>A doctoral candidate pursuing the beauty of life.</p>
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<ul class="list-inline">
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