1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
|
<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>AnalyseMapping</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<h1 class="toc">Module AnalyseMapping</h1>
<hr />
<h2 class="toc">Classes</h2>
<a target="mainFrame" href="core.AnalyseMapping.CustomRead-class.html"
>CustomRead</a><br /> <a target="mainFrame" href="core.AnalyseMapping.ReadID-class.html"
>ReadID</a><br /> <a target="mainFrame" href="core.AnalyseMapping.TPRead-class.html"
>TPRead</a><br /> <h2 class="toc">Functions</h2>
<a target="mainFrame" href="core.AnalyseMapping-module.html#CheckForSameAlignments"
>CheckForSameAlignments</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#CompareAlignments"
>CompareAlignments</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#ComputeRQScore"
>ComputeRQScore</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#CreateCompareList"
>CreateCompareList</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#GetCompletePath"
>GetCompletePath</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#GetOrderDictionary"
>GetOrderDictionary</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#ReadArtificialSAMfileHTSeq"
>ReadArtificialSAMfileHTSeq</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#ReadFromTab"
>ReadFromTab</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#ReadSAMnoMem"
>ReadSAMnoMem</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#SkipHeader"
>SkipHeader</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#extendReadDic"
>extendReadDic</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getAlignmentLength"
>getAlignmentLength</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getAllID"
>getAllID</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getCustomRead"
>getCustomRead</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getHammingdistance"
>getHammingdistance</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getMisGap"
>getMisGap</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getNextLine"
>getNextLine</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getNumberOf"
>getNumberOf</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getRanks"
>getRanks</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getTPRead"
>getTPRead</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getmean"
>getmean</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#getsum"
>getsum</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#initOutFiles"
>initOutFiles</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#isSaneAlignment"
>isSaneAlignment</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#loadpickle"
>loadpickle</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#readInput"
>readInput</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#readReadQualities"
>readReadQualities</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#readSAMline"
>readSAMline</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#returnIndex"
>returnIndex</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#returnSequence"
>returnSequence</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#savepickle"
>savepickle</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#writeToTabArt"
>writeToTabArt</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#writeToTabRef"
>writeToTabRef</a><br /> <h2 class="toc">Variables</h2>
<a target="mainFrame" href="core.AnalyseMapping-module.html#AlignedReadsdic"
>AlignedReadsdic</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#__package__"
>__package__</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#algnedToArt"
>algnedToArt</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#algnedToRef"
>algnedToRef</a><br /> <a target="mainFrame" href="core.AnalyseMapping-module.html#alngts"
>alngts</a><br /><hr />
<span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
|
