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
74
75
76
77
78
79
80
81
|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.14"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>iVar: src/alignment.h Source File</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">iVar
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.14 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */
var searchBox = new SearchBox("searchBox", "search",false,'Search');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">alignment.h</div> </div>
</div><!--header-->
<div class="contents">
<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#include<iostream></span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#include <algorithm></span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include<vector></span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include<fstream></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include<ctime></span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> </div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> </div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor">#ifndef primer_bed</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#define primer_bed</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> </div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">/* Substitution Matrix</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"></span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> A T G C N</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">A 1 -1 -1 -1 0</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">T -1 1 -1 -1 0</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">G -1 -1 1 -1 0</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">C -1 -1 -1 1 0</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">N 0 0 0 0 0</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">*/</span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="keyword">const</span> <span class="keywordtype">int</span> unit_score = 2;</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> </div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="keyword">const</span> <span class="keywordtype">int</span> substitution[5][5] = {</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  {unit_score,-unit_score,-unit_score,-unit_score, 0},</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  {-unit_score,unit_score,-unit_score,-unit_score, 0},</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  {-unit_score,-unit_score,unit_score,-unit_score, 0},</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  {-unit_score,-unit_score,-unit_score,unit_score, 0},</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  {0, 0, 0, 0, 0}</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> };</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> </div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="keyword">const</span> <span class="keywordtype">int</span> gap_open = unit_score - 1;</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="keyword">const</span> <span class="keywordtype">int</span> gap_extension = -1;</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="keyword">const</span> <span class="keywordtype">int</span> max_read_size = 500;</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">const</span> <span class="keywordtype">int</span> max_adapter_size = 60;</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">const</span> <span class="keywordtype">int</span> MAX_GAP = 2;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> </div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keywordtype">int</span> get_sub_score(<span class="keywordtype">char</span> a, <span class="keywordtype">char</span> b);</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="keywordtype">int</span> get_gap_penalty(<span class="keywordtype">int</span> k, <span class="keywordtype">char</span> a);</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="keywordtype">void</span> print_matrix(<span class="keywordtype">int</span> h[][max_adapter_size], <span class="keywordtype">int</span> r, <span class="keywordtype">int</span> c, std::string read, std::string adap);</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keywordtype">int</span>* get_score_cell(<span class="keywordtype">int</span> h[][max_adapter_size], <span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j, std::string read, std::string adap);</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="keywordtype">void</span> print_alignment(<span class="keywordtype">char</span> a[2][max_read_size], <span class="keywordtype">int</span> n);</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="keywordtype">int</span>* align_seqs(std::string read, std::string adap);</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keywordtype">int</span> find_adapters_contaminants(std::istream &cin, std::string adp_cntms_file);</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="keywordtype">int</span> <a class="code" href="ivar_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a>(<span class="keywordtype">int</span> argc, <span class="keywordtype">char</span>* argv[]);</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#endif</span></div><div class="ttc" id="ivar_8cpp_html_a0ddf1224851353fc92bfbff6f499fa97"><div class="ttname"><a href="ivar_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a></div><div class="ttdeci">int main(int argc, char *argv[])</div><div class="ttdef"><b>Definition:</b> ivar.cpp:144</div></div>
</div><!-- fragment --></div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.14
</small></address>
</body>
</html>
|
