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
82
|
<!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/call_consensus_pileup.cpp 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">call_consensus_pileup.cpp</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<fstream></span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include<sstream></span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include<vector></span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include<algorithm></span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#include<string></span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#include<regex></span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> </div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#include "allele_functions.h"</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#include "call_consensus_pileup.h"</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> </div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="keyword">const</span> std::string gap=<span class="stringliteral">"N"</span>;</div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> </div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="keywordtype">void</span> format_alleles(std::vector<allele> &ad){</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  std::vector<allele>::iterator it = ad.begin();</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  <span class="keywordtype">int</span> prev_ind = 0;</div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  <span class="keywordflow">while</span>(it < ad.end()){</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  <span class="keywordflow">if</span>(it->nuc[0] == <span class="charliteral">'-'</span>){ <span class="comment">// Remove deletions</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  it = ad.erase(it);</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  } <span class="comment">// else if (it->nuc[0] == '+'){</span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <span class="comment">// it->nuc[0] = it->prev_base;</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  <span class="comment">// prev_ind = find_ref_in_allele(ad, it->prev_base);</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="comment">// if(prev_ind!=-1)</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  <span class="comment">// ad.at(prev_ind).depth -= it->depth;</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  <span class="comment">// }</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  ++it;</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  }</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> }</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> <span class="keywordtype">bool</span> compare_allele_depth(<span class="keyword">const</span> <a class="code" href="structallele.html">allele</a> &a, <span class="keyword">const</span> <a class="code" href="structallele.html">allele</a> &b){</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keywordflow">return</span> b.depth < a.depth;</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> }</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <a class="code" href="structret__t.html">ret_t</a> get_consensus_allele(std::vector<allele> ad, uint8_t min_qual, <span class="keywordtype">double</span> threshold){</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <a class="code" href="structret__t.html">ret_t</a> t;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  t.nuc=<span class="stringliteral">""</span>;</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  t.q = min_qual+33;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordflow">if</span>(ad.size()==0)</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="keywordflow">return</span> t;</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  format_alleles(ad);</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordflow">if</span>(ad.size() == 1){</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  t.nuc = (ad.at(0).nuc.compare(<span class="stringliteral">"*"</span>) == 0) ? <span class="stringliteral">""</span> : ad.at(0).nuc;</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  t.q = (ad.at(0).nuc.compare(<span class="stringliteral">"*"</span>) == 0) ? min_qual + 33 : ad.at(0).mean_qual + 33;</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordflow">return</span> t;</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>  std::string cnuc = <span class="stringliteral">""</span>;</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  std::vector<allele> nuc_pos;</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <a class="code" href="structallele.html">allele</a> tmp_a;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordtype">char</span> n;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  uint32_t max_l = 0, max_depth = 0, tmp_depth = 0, cur_depth = 0, total_max_depth = 0, gap_depth = 0, total_indel_depth = 0;</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  uint8_t ambg_n = 1, ctr = 0;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordtype">double</span> q = 0, tq = 0, cur_threshold = 0;</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  std::vector<allele>::iterator it;</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keywordflow">for</span>(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordflow">if</span>(it->nuc.length() > max_l){</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  max_l = it->nuc.length();</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  }</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordflow">if</span>(it->nuc.length() == 1){</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  total_max_depth += it->depth;</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  total_indel_depth += it->depth;</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  total_indel_depth = total_indel_depth - it->end; <span class="comment">// For indels</span></div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  }</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  }</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  t.nuc = <span class="stringliteral">""</span>;</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  t.q = <span class="stringliteral">""</span>;</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordflow">for</span> (uint16_t i = 0; i < max_l; ++i){</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  n = <span class="charliteral">'*'</span>;</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  q = 0;</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  tq = 0;</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  max_depth = 0;</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  tmp_depth = 0;</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  cur_depth = 0;</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="comment">// prev_depth = 0;</span></div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  ctr = 1;</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  it = ad.begin();</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  gap_depth = 0;</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  nuc_pos.clear();</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordflow">while</span>(it!=ad.end()){</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordflow">if</span>(!(i < it->nuc.length())){</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  it++;</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  }</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keywordflow">if</span>(it->nuc[i] == <span class="charliteral">'+'</span> || it->nuc[i] == <span class="charliteral">'-'</span>){</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  it++;</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  }</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  tmp_depth = it->depth;</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  tq = it->mean_qual;</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  ctr = 1;</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keywordflow">while</span>(it!=ad.end()-1 && i < (it+1)->nuc.length() && it->nuc[i] == (it+1)->nuc[i]){ <span class="comment">// Third condition for cases with more than 1 base in insertion && (i+1) < (it+1)->nuc.length()</span></div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  tmp_depth += (it+1)->depth;</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  tq = ((tq * (ctr)) + (it+1)->mean_qual)/(ctr + 1);</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  it++;</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  ctr++;</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  }</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  cur_depth += tmp_depth;</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  tmp_a.nuc = it->nuc[i];</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  tmp_a.mean_qual = tq;</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  tmp_a.reverse = 0; <span class="comment">// Reverse reads not important for consensus</span></div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  tmp_a.depth = tmp_depth;</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  nuc_pos.push_back(tmp_a);</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="comment">// if(tmp_depth > max_depth){</span></div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// n = it->nuc[i];</span></div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="comment">// max_depth = tmp_depth;</span></div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="comment">// q = tq;</span></div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="comment">// ambg_n = 1;</span></div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="comment">// } else if(tmp_depth == max_depth){</span></div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="comment">// n = gt2iupac(n, it->nuc[i]);</span></div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="comment">// q = ((q * ambg_n) + tq)/(ambg_n+1);</span></div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="comment">// ambg_n += 1;</span></div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="comment">// }</span></div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  it++;</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  }</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="comment">// Sort nuc_pos by depth of alleles</span></div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  std::sort(nuc_pos.begin(), nuc_pos.end(), compare_allele_depth);</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  it=nuc_pos.begin();</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  n = it->nuc[0];</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  q = it->mean_qual;</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  max_depth = it->depth;</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  it++;</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  ambg_n = 1;</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordflow">if</span>(i > 0){</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  cur_threshold = threshold * (double) total_indel_depth;</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  cur_threshold = threshold * (double)total_max_depth;</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  }</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordflow">while</span>(it!=nuc_pos.end() && (max_depth < cur_threshold || it->depth == (it -1)->depth)){ <span class="comment">// Iterate till end or till cross threshold and no more allele with same depth</span></div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  n = gt2iupac(n, it->nuc[0]);</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  q = ((q * ambg_n) + it->mean_qual)/(ambg_n+1);</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  ambg_n += 1;</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  max_depth += it->depth;</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  it++;</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  }</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordflow">if</span>(max_depth < cur_threshold) <span class="comment">// If depth still less than threshold</span></div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  n = <span class="charliteral">'N'</span>;</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordflow">if</span>(i > 0)</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  gap_depth = (total_indel_depth > cur_depth) ? total_indel_depth - cur_depth : 0;</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  gap_depth = 0; <span class="comment">// For first position of allele</span></div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordflow">if</span>(n!=<span class="charliteral">'*'</span> && max_depth >= gap_depth){ <span class="comment">// TODO: Check what to do when equal.{</span></div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  t.nuc += n;</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  q += 0.5; <span class="comment">// For rounding before converting to int</span></div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  t.q += (((uint8_t)q)+33);</div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  }</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  }</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordflow">return</span> t;</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span> }</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span> <span class="keywordtype">int</span> call_consensus_from_plup(std::istream &cin, std::string out_file, uint8_t min_qual, <span class="keywordtype">double</span> threshold){</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  std::string line, cell;</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  std::ofstream fout(out_file+<span class="stringliteral">".fa"</span>);</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  std::ofstream tmp_qout(out_file+<span class="stringliteral">".qual.txt"</span>);</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  fout << <span class="stringliteral">">Consensus"</span> << <span class="stringliteral">"_"</span> << threshold <<std::endl;</div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keywordtype">int</span> ctr = 0, pos = 0, mdepth = 0;</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  std::stringstream lineStream;</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keywordtype">char</span> ref;</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  std::string bases;</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  std::string qualities;</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  std::vector<allele> ad;</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordflow">while</span> (std::getline(cin, line)){</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  lineStream << line;</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  ctr = 0;</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordflow">while</span>(std::getline(lineStream,cell,<span class="charliteral">'\t'</span>)){</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="keywordflow">switch</span>(ctr){</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">case</span> 0:</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordflow">case</span> 1:</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  pos = stoi(cell);</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordflow">case</span> 2:</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  ref = cell[0];</div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordflow">case</span> 3:</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  mdepth = stoi(cell);</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="keywordflow">case</span> 4:</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  bases = cell;</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordflow">case</span> 5:</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  qualities = cell;</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keywordflow">case</span> 6:</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  }</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  ctr++;</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  }</div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  ad = update_allele_depth(ref, bases, qualities, min_qual);</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <a class="code" href="structret__t.html">ret_t</a> t = get_consensus_allele(ad, min_qual, threshold);</div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  fout << t.nuc;</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  tmp_qout << t.q;</div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  lineStream.clear();</div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  ad.clear();</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  }</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  tmp_qout.close();</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  fout.close();</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span> }</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> </div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span> <span class="comment">// int main_old(int argc, char* argv[]) {</span></div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span> <span class="comment">// std::string line, cell;</span></div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span> <span class="comment">// std::string out_file = argv[1];</span></div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span> <span class="comment">// uint8_t min_qual = 20;</span></div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span> <span class="comment">// if(argc > 1){</span></div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span> <span class="comment">// min_qual = atoi(argv[2]);</span></div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span> <span class="comment">// }</span></div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span> <span class="comment">// std::ofstream fout(out_file+".fa");</span></div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span> <span class="comment">// fout << ">Consensus"<<std::endl;</span></div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span> <span class="comment">// int ctr = 0, pos = 0, mdepth = 0;</span></div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span> <span class="comment">// std::stringstream lineStream;</span></div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span> <span class="comment">// char ref;</span></div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span> <span class="comment">// std::string bases;</span></div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span> <span class="comment">// std::string qualities;</span></div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span> <span class="comment">// std::vector<allele> ad;</span></div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span> <span class="comment">// while (std::getline(std::cin, line)){</span></div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span> <span class="comment">// lineStream << line;</span></div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span> <span class="comment">// ctr = 0;</span></div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span> <span class="comment">// while(std::getline(lineStream,cell,'\t')){</span></div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span> <span class="comment">// switch(ctr){</span></div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span> <span class="comment">// case 0:</span></div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span> <span class="comment">// break;</span></div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span> <span class="comment">// case 1:</span></div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span> <span class="comment">// pos = stoi(cell);</span></div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span> <span class="comment">// break;</span></div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span> <span class="comment">// case 2:</span></div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span> <span class="comment">// ref = cell[0];</span></div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span> <span class="comment">// break;</span></div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span> <span class="comment">// case 3:</span></div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span> <span class="comment">// mdepth = stoi(cell);</span></div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span> <span class="comment">// break;</span></div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span> <span class="comment">// case 4:</span></div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span> <span class="comment">// bases = cell;</span></div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span> <span class="comment">// break;</span></div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span> <span class="comment">// case 5:</span></div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span> <span class="comment">// qualities = cell;</span></div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span> <span class="comment">// break;</span></div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span> <span class="comment">// case 6:</span></div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span> <span class="comment">// break;</span></div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span> <span class="comment">// }</span></div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span> <span class="comment">// ctr++;</span></div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span> <span class="comment">// }</span></div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span> <span class="comment">// ad = update_allele_depth(ref, bases, qualities, min_qual);</span></div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span> <span class="comment">// // print_allele_depths(ad);</span></div><div class="line"><a name="l00243"></a><span class="lineno"> 243</span> <span class="comment">// fout << get_consensus_allele(ad);</span></div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span> <span class="comment">// // std::cout << std::endl << "Consensus: " << get_consensus_allele(ad) << std::endl;</span></div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span> <span class="comment">// lineStream.clear();</span></div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span> <span class="comment">// }</span></div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span> <span class="comment">// fout.close();</span></div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span> <span class="comment">// return 0;</span></div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span> <span class="comment">// }</span></div><div class="ttc" id="structret__t_html"><div class="ttname"><a href="structret__t.html">ret_t</a></div><div class="ttdef"><b>Definition:</b> <a href="call__consensus__pileup_8h_source.html#l00007">call_consensus_pileup.h:7</a></div></div>
<div class="ttc" id="structallele_html"><div class="ttname"><a href="structallele.html">allele</a></div><div class="ttdef"><b>Definition:</b> <a href="allele__functions_8h_source.html#l00007">allele_functions.h:7</a></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>
|
