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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#include "htslib/vcf.h"</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> </div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include<iostream></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> </div><div class="line"><a name="l00006"></a><span class="lineno"><a class="line" href="structmaj.html"> 6</a></span> <span class="keyword">struct </span><a class="code" href="structmaj.html">maj</a> {</div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span>  <span class="keywordtype">int</span> *ind;</div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span>  <span class="keywordtype">int</span> n;</div><div class="line"><a name="l00009"></a><span class="lineno"> 9</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="preprocessor">#define GET_MAX_INDICES(type_t, pu, no, m) { \</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor"> type_t v = 1; \</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor"> type_t *p = (type_t*) (pu); \</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor"> for (int k = 0; k < no; ++k){ \</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor"> if(p[k] > v){ \</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor"> v = p[k]; \</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor"> m.n = 0; \</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor"> m.ind[m.n] = k; \</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor"> } else if(p[k] == v) { \</span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor"> m.n++; \</span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor"> m.ind[m.n] = k; \</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor"> } \</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor"> } \</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor"> }</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#define INDEL_SIZE 30</span></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> <span class="preprocessor">#define GAP 'N'</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="comment">// From bcftools.h - https://github.com/samtools/bcftools/blob/b0376dff1ed70603c9490802f37883b9009215d2/bcftools.h#L48</span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">char</span> gt2iupac(<span class="keywordtype">char</span> a, <span class="keywordtype">char</span> b)</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>  <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> iupac[4][4] = { {<span class="charliteral">'A'</span>,<span class="charliteral">'M'</span>,<span class="charliteral">'R'</span>,<span class="charliteral">'W'</span>},{<span class="charliteral">'M'</span>,<span class="charliteral">'C'</span>,<span class="charliteral">'S'</span>,<span class="charliteral">'Y'</span>},{<span class="charliteral">'R'</span>,<span class="charliteral">'S'</span>,<span class="charliteral">'G'</span>,<span class="charliteral">'K'</span>},{<span class="charliteral">'W'</span>,<span class="charliteral">'Y'</span>,<span class="charliteral">'K'</span>,<span class="charliteral">'T'</span>} };</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordflow">if</span> ( a>=<span class="charliteral">'a'</span> ) a -= <span class="charliteral">'a'</span> - <span class="charliteral">'A'</span>;</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordflow">if</span> ( b>=<span class="charliteral">'a'</span> ) b -= <span class="charliteral">'a'</span> - <span class="charliteral">'A'</span>;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keywordflow">if</span> ( a==<span class="charliteral">'A'</span> ) a = 0;</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> ( a==<span class="charliteral">'C'</span> ) a = 1;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> ( a==<span class="charliteral">'G'</span> ) a = 2;</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> ( a==<span class="charliteral">'T'</span> ) a = 3;</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keywordflow">else</span> <span class="keywordflow">return</span> <span class="charliteral">'N'</span>;</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordflow">if</span> ( b==<span class="charliteral">'A'</span> ) b = 0;</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> ( b==<span class="charliteral">'C'</span> ) b = 1;</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> ( b==<span class="charliteral">'G'</span> ) b = 2;</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> ( b==<span class="charliteral">'T'</span> ) b = 3;</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordflow">else</span> <span class="keywordflow">return</span> <span class="charliteral">'N'</span>;</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordflow">return</span> iupac[(int)a][(<span class="keywordtype">int</span>)b];</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> }</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="keywordtype">void</span> get_consensus_indel(<span class="keywordtype">char</span> **<a class="code" href="structallele.html">allele</a>, <a class="code" href="structmaj.html">maj</a> m, <span class="keywordtype">char</span> *&nuc){</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordtype">int</span> max_len = 0, l = 0;</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  uint8_t q = 0;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> k = 0; k <= m.n; ++k){</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keywordflow">if</span>(strlen(<a class="code" href="structallele.html">allele</a>[m.ind[k]]) > max_len)</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  max_len = strlen(<a class="code" href="structallele.html">allele</a>[m.ind[k]]);</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  }</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordtype">char</span> n;</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> j = 0; j < max_len; ++j){ <span class="comment">// Iterate over base positions</span></div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  n = 0;</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> k = 0; k <= m.n ; ++k){ <span class="comment">// Iterate over major alleles</span></div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordflow">if</span>(j < strlen(<a class="code" href="structallele.html">allele</a>[m.ind[k]])){</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordflow">if</span>(n == 0){</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  n = <a class="code" href="structallele.html">allele</a>[m.ind[k]][j];</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  n = gt2iupac(n, <a class="code" href="structallele.html">allele</a>[m.ind[k]][j]);</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  }</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  }</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  }</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordflow">if</span>(n == 0)</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  nuc[l] = GAP;</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  nuc[l] = n;</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  l++;</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordflow">if</span>(l % INDEL_SIZE == 0){</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  nuc = (<span class="keywordtype">char</span>*) realloc(nuc, INDEL_SIZE * ((l/INDEL_SIZE) + 1) * <span class="keyword">sizeof</span>(char));</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  }</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  }</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  nuc[l] = 0;</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> }</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="keywordtype">int</span> main_old(<span class="keywordtype">int</span> argc, <span class="keywordtype">char</span>* argv[]) {</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  std::cout << <span class="stringliteral">"Path "</span> << argv[1] <<std::endl;</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  std::string bcf = std::string(argv[1]);</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  std::string region_;</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  std::string out_path = std::string(argv[2]);</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordflow">if</span>(argc > 3) {</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  region_ = std::string(argv[3]);</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  }</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordflow">if</span>(!bcf.empty()) {</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="comment">//open BCF for reading</span></div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  htsFile *in = bcf_open(bcf.c_str(), <span class="stringliteral">"r"</span>);</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  std::ofstream out(out_path);</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  out << <span class="stringliteral">">"</span> << out_path << <span class="stringliteral">"\n"</span>;</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordflow">if</span>(in == NULL) {</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Unable to open BCF/VCF file."</span>);</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>  <span class="keywordtype">int</span> ad_id;</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="comment">//Get the header</span></div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  bcf_hdr_t *header = bcf_hdr_read(in);</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keywordflow">if</span>(header == NULL) {</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  bcf_close(in);</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Unable to open BCF header."</span>);</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  }</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  ad_id = bcf_hdr_id2int(header, BCF_DT_ID, <span class="stringliteral">"AD"</span>);</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  std::cout << ad_id << <span class="stringliteral">" "</span> << std::endl;</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="comment">//Initialize iterator</span></div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  bcf1_t *v = bcf_init();</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordtype">int</span> ctr = 0, prev_pos = 0, s, d;</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <a class="code" href="structmaj.html">maj</a> m;</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordtype">char</span> *nuc =(<span class="keywordtype">char</span> *) malloc(INDEL_SIZE * <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>)), *r;</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordflow">while</span>(bcf_read(in, header, v) ==0){</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="comment">// std::cout << "Position: " << v->pos << std::endl;</span></div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="comment">// std::cout << "Number of Alleles: " << v->n_allele << std::endl;</span></div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = prev_pos; i < v->pos - 1; ++i){</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  out << GAP;</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  }</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  bcf_unpack(v, BCF_UN_FMT);</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  bcf_unpack(v, BCF_UN_STR);</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  bcf_fmt_t *fmt = v->d.fmt;</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < v->n_fmt; ++i){</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordflow">if</span>(strcmp(header->id[BCF_DT_ID][fmt[i].id].key, <span class="stringliteral">"AD"</span>) == 0){</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  m.ind = (<span class="keywordtype">int</span> *) malloc(fmt[i].n * <span class="keyword">sizeof</span>(<span class="keywordtype">int</span>));</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  m.n = -1;</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordflow">switch</span>(fmt[i].type){</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordflow">case</span> BCF_BT_INT8: GET_MAX_INDICES(int8_t, fmt[i].p, fmt[i].n, m); <span class="keywordflow">break</span>;</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordflow">case</span> BCF_BT_INT16: GET_MAX_INDICES(int16_t, fmt[i].p, fmt[i].n, m); <span class="keywordflow">break</span>;</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordflow">case</span> BCF_BT_INT32: GET_MAX_INDICES(int32_t, fmt[i].p, fmt[i].n, m); <span class="keywordflow">break</span>;</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordflow">case</span> BCF_BT_FLOAT: GET_MAX_INDICES(<span class="keywordtype">float</span>, fmt[i].p, fmt[i].n, m); <span class="keywordflow">break</span>;</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordflow">default</span>: hts_log_error(<span class="stringliteral">"Unexpected type %d"</span>, fmt[i].type); exit(1);</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  }</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordflow">if</span>(m.n == -1){</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  out << GAP;</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordflow">if</span>(bcf_get_variant_types(v) == VCF_REF){</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  out << v->d.allele[0];</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span>(bcf_get_variant_types(v) == VCF_SNP || bcf_get_variant_types(v) == VCF_MNP){</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  nuc =(<span class="keywordtype">char</span> *) malloc(INDEL_SIZE * <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>));</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  get_consensus_indel(v->d.allele, m, nuc);</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  out << nuc;</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  } <span class="keywordflow">else</span> { <span class="comment">// For INDEL insert difference.between reference and consensus allele</span></div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  nuc =(<span class="keywordtype">char</span> *) malloc(INDEL_SIZE * <span class="keyword">sizeof</span>(<span class="keywordtype">char</span>));</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  get_consensus_indel(v->d.allele, m, nuc);</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  s = strlen(v->d.allele[0]) - strlen(nuc); <span class="comment">// > 0 Deletion. < 0 INSERTION</span></div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  d = (s > 0) ? strlen(v->d.allele[0]) : strlen(nuc);</div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  r = (s > 0) ? v->d.allele[0] : nuc;</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  s = (s < 0) ? -1 * s : s;</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordflow">if</span>(v->pos == 499)</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  std::cout << <span class="stringliteral">"Number: "</span> << m.n << <span class="stringliteral">" Maj Allele: "</span> << v->d.allele[m.ind[0]] << strlen(nuc) << <span class="stringliteral">" - Nuc Length"</span> << nuc << <span class="stringliteral">" "</span> << s << <span class="stringliteral">" "</span> << d << std::endl;</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < s; ++i){</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  out << r[d - s];</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  }</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  free(m.ind);</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  free(nuc);</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="comment">// std::cout << nuc << std::endl;</span></div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  }</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  }</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  }</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  }</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  prev_pos = v->pos;</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  ctr++;</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordflow">if</span>(ctr % 1000 == 0){</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  std::cout << ctr << std::endl;</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  }</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  }</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  bcf_destroy(v);</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  bcf_hdr_destroy(header);</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  bcf_close(in);</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  out.close();</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  }</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span> }</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 class="ttc" id="structmaj_html"><div class="ttname"><a href="structmaj.html">maj</a></div><div class="ttdef"><b>Definition:</b> <a href="call__consensus_8cpp_source.html#l00006">call_consensus.cpp:6</a></div></div>
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