html文件下的flag,推荐一个SAM文件中flag含义解释工具

SAM是Sequence Alignment/Map 的缩写。像bwa等软件序列比对结果都会输出这样的文件。samtools网站上有专门的文档介绍SAM文件。具体地址&＃xff1a;http://samtools.sourceforge.net/SAM1.pdf

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&＃xff0c;但是为了方便大家&＃xff0c;下面给大家提供一个脚本工具&＃xff0c;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&＃xff1a;

脚本工具的使用方法&＃xff1a;

将下面的代码保存在记事本里面&＃xff0c;另存为一个html文件&＃xff0c;如文件名&＃xff1a;FlagExplain.html(拓展名一定要为.html)。双击既可以在浏览器里面打开了。

lstFlags &＃61; [["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 &＃61; parseInt(document.getElementById(&＃39;tb&＃39;).value); //returns 0 or NaN if can&＃39;t parse

var summary &＃61; "";

for(var i &＃61; 0; i

var checkbox &＃61; document.getElementById(&＃39;cb&＃39; &＃43; i)

if(lstFlags[i][1] & flagValue) {

summary &＃43;&＃61; "     " &＃43; lstFlags[i][0] &＃43; "
";

checkbox.checked &＃61; true;

} else {

checkbox.checked &＃61; false;

}

}

document.getElementById(&＃39;summary&＃39;).innerHTML &＃61; summary;

}

function checkboxClicked() {

//compute the new flag value

var newFlagValue &＃61; 0;

for(var i &＃61; 0; i

var checkBox &＃61; document.getElementById(&＃39;cb&＃39; &＃43; i);

if(checkBox.checked) {

newFlagValue |&＃61; lstFlags[i][1];

}

}

var textbox &＃61; document.getElementById(&＃39;tb&＃39;);

textbox.value &＃61; newFlagValue;

explainFlags();

}

This utility explains SAM flags in plain English.

Flag:  

Explanation:

for(var i &＃61; 0; i

document.write("   " &＃43;lstFlags[i][0] &＃43; "
");

}

  read paired   read mapped in proper pair   read unmapped   mate unmapped   read reverse strand   mate reverse strand   first in pair   second in pair   not primary alignment   read fails platform/vendor quality checks   read is PCR or optical duplicate

Summary: