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<div class="title">remove_reads_from_amplicon.cpp</div> </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#include "primer_bed.h"</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#include "htslib/sam.h"</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include "htslib/bgzf.h"</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> </div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include<iostream></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> <span class="keywordtype">int</span> rmv_reads_from_amplicon(std::string bam, std::string region_, std::string bam_out, uint16_t* amplicon, <span class="keywordtype">int</span> amp_n){</div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < amp_n; ++i){</div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span>  std::cout << <span class="stringliteral">"Amplicon: "</span> << amplicon[i] << <span class="stringliteral">" "</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>  bam_out += <span class="stringliteral">".bam"</span>;</div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  std::cout << std::endl;</div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  std::cout << bam_out << std::endl;</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  <span class="keywordflow">if</span>(bam.empty()){</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  std::cout << <span class="stringliteral">"Bam in empty"</span> << std::endl;</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  }</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  <span class="comment">//open BAM for reading</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  samFile *in = hts_open(bam.c_str(), <span class="stringliteral">"r"</span>);</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  BGZF *out = bgzf_open(bam_out.c_str(), <span class="stringliteral">"w"</span>);</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <span class="keywordflow">if</span>(in == NULL) {</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  std::cout << (<span class="stringliteral">"Unable to open BAM/SAM file."</span>) << std::endl;</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  }</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  <span class="comment">//Load the index</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  hts_idx_t *idx = sam_index_load(in, bam.c_str());</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="keywordflow">if</span>(idx == NULL) {</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  std::cout << (<span class="stringliteral">"Unable to open BAM/SAM index."</span>) << std::endl; <span class="comment">// TODO: Generate index</span></div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordflow">return</span> -1;</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="comment">//Get the header</span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  bam_hdr_t *header = sam_hdr_read(in);</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordflow">if</span>(bam_hdr_write(out, header) < 0){</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  std::cout << <span class="stringliteral">"Unable to write BAM header to path."</span> << std::endl;</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  sam_close(in);</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  }</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordflow">if</span>(header == NULL) {</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  sam_close(in);</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  std::cout << <span class="stringliteral">"Unable to open BAM/SAM header."</span> << std::endl;</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  }</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordflow">if</span> (region_.empty()){</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  std::cout << <span class="stringliteral">"Number of references: "</span> << header->n_targets << std::endl;</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < header->n_targets; ++i){</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  std::cout << <span class="stringliteral">"Reference Name: "</span> << header->target_name[i] << std::endl;</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  std::cout << <span class="stringliteral">"Reference Length: "</span> << header->target_len[i] << std::endl;</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordflow">if</span>(i==0){</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  region_.assign(header->target_name[i]);</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  }</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  }</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  std::cout << <span class="stringliteral">"Using Region: "</span> << region_ << std::endl;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  }</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  std::string temp(header->text);</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  std::string sortFlag (<span class="stringliteral">"SO:coordinate"</span>);</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordflow">if</span> (temp.find(sortFlag)) {</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  std::cout << <span class="stringliteral">"Sorted By Coordinate"</span> << std::endl; <span class="comment">// Sort by coordinate</span></div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  std::cout << <span class="stringliteral">"Not sorted"</span> << std::endl;</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  }</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="comment">//Initialize iterator</span></div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  hts_itr_t *iter = NULL;</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="comment">//Move the iterator to the region we are interested in</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  iter = sam_itr_querys(idx, header, region_.c_str());</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">if</span>(header == NULL || iter == NULL) {</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  sam_close(in);</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  std::cout << <span class="stringliteral">"Unable to iterate to region within BAM/SAM."</span> << std::endl;</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  }</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="comment">//Initiate the alignment record</span></div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  bam1_t *aln = bam_init1();</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keywordtype">int</span> ctr = 0;</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordtype">bool</span> w;</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordflow">while</span>(sam_itr_next(in, iter, aln) >= 0) {</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  uint8_t* a = bam_aux_get(aln, <span class="stringliteral">"xa"</span>);</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  w = <span class="keyword">true</span>;</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordflow">if</span>(a != 0){</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < amp_n; ++i){</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordflow">if</span>(bam_aux2i(a) == amplicon[i]){</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  w = <span class="keyword">false</span>;</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  }</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</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>(w){</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keywordflow">if</span>(bam_write1(out, aln) < 0){</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  std::cout << <span class="stringliteral">"Not able to write to BAM"</span> << std::endl;</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  hts_itr_destroy(iter);</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  hts_idx_destroy(idx);</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  bam_destroy1(aln);</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  bam_hdr_destroy(header);</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  sam_close(in);</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  bgzf_close(out);</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  };</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  }</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  ctr++;</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keywordflow">if</span>(ctr % 100000 == 0){</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  std::cout << ctr << std::endl;</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  }</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  }</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  hts_itr_destroy(iter);</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  hts_idx_destroy(idx);</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  bam_destroy1(aln);</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  bam_hdr_destroy(header);</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  sam_close(in);</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  bgzf_close(out);</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span> }</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="comment">// int main_old(int argc, char* argv[]){</span></div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span> <span class="comment">// std::string bam = std::string(argv[1]);</span></div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span> <span class="comment">// std::string region_;</span></div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> <span class="comment">// std::string bam_out = std::string(argv[2]);</span></div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> <span class="comment">// argc -= 3;</span></div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> <span class="comment">// std::cout << argc << std::endl;</span></div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span> <span class="comment">// int16_t amplicon[argc];</span></div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="comment">// for (int i = 0; i < argc; ++i){</span></div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="comment">// amplicon[i] = atoi(argv[i+3]); // TODO: Convert to int16_t</span></div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span> <span class="comment">// }</span></div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="comment">// for (int i = 0; i < sizeof(amplicon)/sizeof(*amplicon); ++i){</span></div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="comment">// std::cout << "Amplicon: " << amplicon[i] << " ";</span></div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span> <span class="comment">// }</span></div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span> <span class="comment">// std::cout << std::endl;</span></div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> <span class="comment">// std::cout << bam_out << std::endl;</span></div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="comment">// if(!bam.empty()) {</span></div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> <span class="comment">// //open BAM for reading</span></div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> <span class="comment">// samFile *in = hts_open(bam.c_str(), "r");</span></div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> <span class="comment">// BGZF *out = bgzf_open(bam_out.c_str(), "w");</span></div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span> <span class="comment">// if(in == NULL) {</span></div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="comment">// throw std::runtime_error("Unable to open BAM/SAM file.");</span></div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span> <span class="comment">// }</span></div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> <span class="comment">// //Load the index</span></div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="comment">// hts_idx_t *idx = sam_index_load(in, bam.c_str());</span></div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="comment">// if(idx == NULL) {</span></div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span> <span class="comment">// throw std::runtime_error("Unable to open BAM/SAM index."); // Generate index</span></div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> <span class="comment">// }</span></div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> <span class="comment">// //Get the header</span></div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span> <span class="comment">// bam_hdr_t *header = sam_hdr_read(in);</span></div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> <span class="comment">// bam_hdr_write(out, header);</span></div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> <span class="comment">// if(header == NULL) {</span></div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span> <span class="comment">// sam_close(in);</span></div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span> <span class="comment">// throw std::runtime_error("Unable to open BAM header.");</span></div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span> <span class="comment">// }</span></div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> <span class="comment">// if (region_.empty()){</span></div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span> <span class="comment">// std::cout << "Number of references: " << header->n_targets << std::endl;</span></div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span> <span class="comment">// for (int i = 0; i < header->n_targets; ++i){</span></div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span> <span class="comment">// std::cout << "Reference Name: " << header->target_name[i] << std::endl;</span></div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="comment">// std::cout << "Reference Length: " << header->target_len[i] << std::endl;</span></div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span> <span class="comment">// if(i==0){</span></div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span> <span class="comment">// region_.assign(header->target_name[i]);</span></div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span> <span class="comment">// }</span></div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span> <span class="comment">// }</span></div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span> <span class="comment">// std::cout << "Using Region: " << region_ << std::endl;</span></div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span> <span class="comment">// }</span></div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span> <span class="comment">// std::string temp(header->text);</span></div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span> <span class="comment">// std::string sortFlag ("SO:coordinate");</span></div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span> <span class="comment">// if (temp.find(sortFlag)) {</span></div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span> <span class="comment">// std::cout << "Sorted By Coordinate" << std::endl; // Sort by coordinate</span></div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span> <span class="comment">// } else {</span></div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span> <span class="comment">// std::cout << "Not sorted" << std::endl;</span></div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> <span class="comment">// }</span></div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <span class="comment">// //Initialize iterator</span></div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span> <span class="comment">// hts_itr_t *iter = NULL;</span></div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span> <span class="comment">// //Move the iterator to the region we are interested in</span></div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="comment">// iter = sam_itr_querys(idx, header, region_.c_str());</span></div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span> <span class="comment">// if(header == NULL || iter == NULL) {</span></div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span> <span class="comment">// sam_close(in);</span></div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span> <span class="comment">// throw std::runtime_error("Unable to iterate to region within BAM.");</span></div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span> <span class="comment">// }</span></div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="comment">// //Initiate the alignment record</span></div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span> <span class="comment">// bam1_t *aln = bam_init1();</span></div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span> <span class="comment">// int ctr = 0;</span></div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span> <span class="comment">// bool w;</span></div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span> <span class="comment">// while(sam_itr_next(in, iter, aln) >= 0) {</span></div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span> <span class="comment">// // std::cout << "Query Length: " << bam_cigar2qlen(aln->core.n_cigar, cigar) << std::endl;</span></div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span> <span class="comment">// // std::cout << "Read Length: " << bam_cigar2rlen(aln->core.n_cigar, cigar) << std::endl;</span></div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span> <span class="comment">// // std::cout << "Query Start: " << get_query_start(aln) << std::endl;</span></div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span> <span class="comment">// // std::cout << "Query End: " << get_query_end(aln) << std::endl</span></div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span> <span class="comment">// uint8_t* a = bam_aux_get(aln, "xa");</span></div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span> <span class="comment">// w = true;</span></div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span> <span class="comment">// for (int i = 0; i < sizeof(amplicon)/sizeof(*amplicon); ++i){</span></div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span> <span class="comment">// if(bam_aux2i(a) == amplicon[i]){</span></div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span> <span class="comment">// w = false;</span></div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span> <span class="comment">// }</span></div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span> <span class="comment">// }</span></div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span> <span class="comment">// if(w)</span></div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span> <span class="comment">// bam_write1(out, aln);</span></div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span> <span class="comment">// ctr++;</span></div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span> <span class="comment">// if(ctr % 100000 == 0){</span></div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span> <span class="comment">// std::cout << ctr << std::endl;</span></div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span> <span class="comment">// }</span></div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span> <span class="comment">// }</span></div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span> <span class="comment">// hts_itr_destroy(iter);</span></div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span> <span class="comment">// hts_idx_destroy(idx);</span></div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span> <span class="comment">// bam_destroy1(aln);</span></div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span> <span class="comment">// bam_hdr_destroy(header);</span></div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span> <span class="comment">// sam_close(in);</span></div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span> <span class="comment">// bgzf_close(out);</span></div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> <span class="comment">// }</span></div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span> <span class="comment">// return 0;</span></div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span> <span class="comment">// }</span></div></div><!-- fragment --></div><!-- contents -->
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