转载：http://www.cnblogs.com/nkwy2012/p/6362996.html
很多人困惑SAM文件中的第二列FLAG值是什么意思。根据文档介绍我们可以计算，但是为了方便大家，下面给大家提供一个脚本工具，大家直接输入flag值就可以知道它代表的含义了。
该脚本的使用方法如下截图所示：
脚本工具的使用方法：
将下面的代码保存在记事本里面，另存为一个html文件，如文件名：FlagExplain.html（拓展名一定要为.html）。双击既可以在浏览器里面打开了。
<html><head><meta http-equiv="Content-Type" content="text/html; charset=GBK">
<title>Explain SAM Flags</title>
<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>
<noscript>This page requires JavaScript. Please enable it in your browser settings.</noscript>
</head>
<body>
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><inputtype="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></html>