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<a href="ivar_8cpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</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 <unistd.h></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"> 6</span> <span class="preprocessor">#include "remove_reads_from_amplicon.h"</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#include "call_consensus_pileup.h"</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor">#include "call_variants.h"</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#include "trim_primer_quality.h"</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#include "get_masked_amplicons.h"</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#include "suffix_tree.h"</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> </div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="keyword">const</span> std::string VERSION = <span class="stringliteral">"1.0"</span>;</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> </div><div class="line"><a name="l00015"></a><span class="lineno"><a class="line" href="structargs__t.html"> 15</a></span> <span class="keyword">struct </span><a class="code" href="structargs__t.html">args_t</a> {</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  std::string bam; <span class="comment">// -i</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  std::string bed; <span class="comment">// -b</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  std::string prefix; <span class="comment">// -p</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  std::string ref; <span class="comment">// -r</span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  std::string region; <span class="comment">// -R</span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  uint8_t min_qual; <span class="comment">// -q</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  uint8_t sliding_window; <span class="comment">// -s</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="keywordtype">double</span> min_threshold; <span class="comment">// -t</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  <span class="keywordtype">int</span> min_length; <span class="comment">// -m</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  std::string f1; <span class="comment">// -1</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  std::string f2; <span class="comment">// -2</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  std::string adp_path; <span class="comment">// -a</span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> } g_args;</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">void</span> print_usage(){</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  std::cout <<</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="stringliteral">"Usage: ivar [command <trim|callvariants|filtervariants|consensus|createbed|getmasked|removereads|version|help>]\n"</span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="stringliteral">"\n"</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="stringliteral">" Command Description\n"</span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="stringliteral">" trim Trim reads in aligned BAMs\n"</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="stringliteral">" variants Call variants from aligned BAM file\n"</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="stringliteral">" filtervariants Filter variants across replicates\n"</span></div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="stringliteral">" consensus Call consensus from aligned BAM file\n"</span></div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="stringliteral">" getmasked Get amplicons with primer mismatches\n"</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="stringliteral">" removereads Remove reads from trimmed BAM file\n"</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="stringliteral">" version Show version information\n"</span></div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="stringliteral">" trimadapter (EXPERIMENTAL) Trim adapter sequences from reads\n"</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="stringliteral">"\n"</span></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="stringliteral">"To view detailed usage for each command type `ivar <command>` \n"</span>;</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> </div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keywordtype">void</span> print_trim_usage(){</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  std::cout <<</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="stringliteral">"Usage: ivar trim -i <input.bam> -b <primers.bed> -p <prefix> [-m <min-length>] [-q <min-quality>] [-s <sliding-window-width>]\n\n"</span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="stringliteral">"Input Options Description\n"</span></div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="stringliteral">" -i (Required) Indexed aligned bam file to trim primers and quality\n"</span></div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="stringliteral">" -b (Required) BED file with primer sequences and positions\n"</span></div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="stringliteral">" -m Minimum length of read to retain after trimming (Default: 30)\n"</span></div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="stringliteral">" -q Minimum quality threshold for sliding window to pass (Default: 20)\n"</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="stringliteral">" -s Width of sliding window (Default: 4)\n\n"</span></div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="stringliteral">"Output Options Description\n"</span></div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="stringliteral">" -p (Required) Prefix for the output BAM file\n"</span>;</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> }</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="keywordtype">void</span> print_variants_usage(){</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  std::cout <<</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="stringliteral">"Usage: samtools mpileup -A -d 300000 --reference <reference-fasta> -Q 0 -F 0 <input.bam> | ivar variants -p <prefix> [-q <min-quality>] [-t <min-frequency-threshold>]\n\n"</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="stringliteral">"Note : samtools mpileup output must be piped into ivar variants\n\n"</span></div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="stringliteral">"Input Options Description\n"</span></div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="stringliteral">" -q Minimum quality score threshold to count base (Default: 20)\n"</span></div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="stringliteral">" -t Minimum frequency threshold(0 - 1) to call variants (Default: 0.03)\n\n"</span></div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="stringliteral">"Output Options Description\n"</span></div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="stringliteral">" -p (Required) Prefix for the output tsv variant file\n\n"</span>;</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> }</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="keywordtype">void</span> print_filtervariants_usage(){</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  std::cout <<</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="stringliteral">"Usage: ivar filtervariants -p <prefix> replicate-one.tsv replicate-two.tsv ... \n\n"</span></div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="stringliteral">"Input: Variant tsv files for each replicate\n\n"</span></div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="stringliteral">"Output Options Description\n"</span></div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="stringliteral">" -p (Required) Prefix for the output filtered tsv file\n"</span>;</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> }</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> <span class="keywordtype">void</span> print_consensus_usage(){</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  std::cout <<</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="stringliteral">"Usage: samtools mpileup -A -d 300000 -Q 0 -F 0 <input.bam> | ivar consensus -p <prefix> \n\n"</span></div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="stringliteral">"Note : samtools mpileup output must be piped into `ivar consensus`\n\n"</span></div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="stringliteral">"Input Options Description\n"</span></div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="stringliteral">" -q Minimum quality score threshold to count base (Default: 20)\n"</span></div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="stringliteral">" -t Minimum frequency threshold(0 - 1) to call consensus. (Default: 0)\n"</span></div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="stringliteral">" Frequently used thresholds | Description\n"</span></div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="stringliteral">" ---------------------------|------------\n"</span></div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="stringliteral">" 0 | Majority or most common base\n"</span></div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="stringliteral">" 0.2 | Bases that make up atleast 20% of the depth at a position\n"</span></div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="stringliteral">" 0.5 | Strict or bases that make up atleast 50% of the depth at a position\n"</span></div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="stringliteral">" 0.9 | Strict or bases that make up atleast 90% of the depth at a position\n"</span></div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="stringliteral">" 1 | Identical or bases that make up 100% of the depth at a position. Will have highest ambiguities\n"</span></div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="stringliteral">"Output Options Description\n"</span></div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="stringliteral">" -p (Required) Prefix for the output fasta file and quality file\n"</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> </div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="keywordtype">void</span> print_removereads_usage(){</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  std::cout <<</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="stringliteral">"Usage: ivar removereads -i <input.trimmed.bam> -p <prefix> primer-index-1 primer-index-2 primer-index-3 primer-index-4 ... \n\n"</span></div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="stringliteral">"Input Options Description\n"</span></div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="stringliteral">" -i (Required) Input BAM file trimmed with ‘ivar trim’. Must be sorted and indexed, which can be done using sort_index_bam.sh\n"</span></div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="stringliteral">"Output Options Description\n"</span></div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="stringliteral">" -p (Required) Prefix for the output filtered BAM file\n"</span>;</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span> }</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span> <span class="keywordtype">void</span> print_getmasked_usage(){</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  std::cout <<</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="stringliteral">"Usage: ivar getmasked -i <input-filtered.tsv> -b <primers.bed>\n\n"</span></div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="stringliteral">"Input Options Description\n"</span></div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="stringliteral">" -i (Required) Input filtered variants tsv generated from `ivar filtervariants`\n"</span></div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="stringliteral">" -b (Required) BED file with primer sequences and positions\n"</span>;</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> }</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="keywordtype">void</span> print_trimadapter_usage(){</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  std::cout <<</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="stringliteral">"Usage: ivar trimadapter [-f1 <input-fastq>] [-f2 <input-fastq-2>] [-p prefix] [-a <adapter-fasta-file>]\n\n"</span></div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="stringliteral">"Input Options Description\n"</span></div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="stringliteral">" -1 (Required) Input fastq file\n"</span></div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="stringliteral">" -2 Input fastq file 2 (for pair ended reads)\n"</span></div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="stringliteral">" -a (Required) Adapter Fasta File\n"</span></div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="stringliteral">" -p (Required) Prefix of output fastq files\n"</span>;</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span> }</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="keywordtype">void</span> print_version_info(){</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  std::cout << <span class="stringliteral">"iVar version "</span> << VERSION << std::endl <<</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="stringliteral">"\nPlease raise issues and bug reports at https://github.com/andersen-lab/ivar/\n"</span>;</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> }</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *trim_opt_str = <span class="stringliteral">"i:b:p:m::q::s::h?"</span>;</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *variants_opt_str = <span class="stringliteral">"p:t::q::h?"</span>;</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *consensus_opt_str = <span class="stringliteral">"p:q::t::h?"</span>;</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *removereads_opt_str = <span class="stringliteral">"i:p:h?"</span>;</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *filtervariants_opt_str = <span class="stringliteral">"p:h?"</span>;</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *getmasked_opt_str = <span class="stringliteral">"i:b:h?"</span>;</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *trimadapter_opt_str = <span class="stringliteral">"1:2::p:a:h?"</span>;</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div><div class="line"><a name="l00144"></a><span class="lineno"><a class="line" href="ivar_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97"> 144</a></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="l00145"></a><span class="lineno"> 145</span>  <span class="keywordflow">if</span>(argc == 1){</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  print_usage();</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordflow">return</span> -1;</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>  std::string cmd(argv[1]);</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordflow">if</span>(cmd.compare(<span class="stringliteral">"-v"</span>) == 0){</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  }</div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keywordtype">int</span> opt = 0, res = 0;</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="comment">// Sift arg by 1 for getopt</span></div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  argv[1] = argv[0];</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  argv++;</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  argc--;</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  g_args.min_qual = 255;</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  g_args.sliding_window = 255;</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  g_args.min_threshold = -1;</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  g_args.min_length = -1;</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordflow">if</span> (cmd.compare(<span class="stringliteral">"trim"</span>) == 0){</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  opt = getopt( argc, argv, trim_opt_str);</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">while</span>( opt != -1 ) {</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="keywordflow">switch</span>( opt ) {</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordflow">case</span> <span class="charliteral">'i'</span>:</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  g_args.bam = optarg;</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> <span class="charliteral">'b'</span>:</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  g_args.bed = optarg;</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> <span class="charliteral">'p'</span>:</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  g_args.prefix = optarg;</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> <span class="charliteral">'m'</span>:</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  g_args.min_length = atoi(optarg);</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> <span class="charliteral">'q'</span>:</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  g_args.min_qual = atoi(optarg);</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> <span class="charliteral">'s'</span>:</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  g_args.sliding_window = atoi(optarg);</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keywordflow">case</span> <span class="charliteral">'h'</span>:</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="keywordflow">case</span> <span class="charliteral">'?'</span>:</div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  print_trim_usage();</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  }</div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  opt = getopt( argc, argv, trim_opt_str);</div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  }</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <span class="keywordflow">if</span>(g_args.bam.empty() || g_args.bed.empty() || g_args.prefix.empty()){</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  print_trim_usage();</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  }</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  g_args.min_qual = (g_args.min_qual == 255) ? 20 : g_args.min_qual;</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  g_args.sliding_window = (g_args.sliding_window == 255) ? 4 : g_args.sliding_window;</div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  g_args.min_length = (g_args.min_length == -1) ? 30 : g_args.min_length;</div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  res = trim_bam_qual_primer(g_args.bam, g_args.bed, g_args.prefix, g_args.region, g_args.min_qual, g_args.sliding_window, g_args.min_length);</div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (cmd.compare(<span class="stringliteral">"variants"</span>) == 0){</div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  opt = getopt( argc, argv, variants_opt_str);</div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="keywordflow">while</span>( opt != -1 ) {</div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keywordflow">switch</span>( opt ) {</div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="keywordflow">case</span> <span class="charliteral">'p'</span>:</div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  g_args.prefix = optarg;</div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="keywordflow">case</span> <span class="charliteral">'t'</span>:</div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  g_args.min_threshold = atof(optarg);</div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordflow">case</span> <span class="charliteral">'q'</span>:</div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  g_args.min_qual = atoi(optarg);</div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordflow">case</span> <span class="charliteral">'h'</span>:</div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  <span class="keywordflow">case</span> <span class="charliteral">'?'</span>:</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  print_variants_usage();</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  }</div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  opt = getopt( argc, argv, variants_opt_str);</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  }</div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="keywordflow">if</span>(g_args.prefix.empty()){</div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  print_variants_usage();</div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  }</div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  g_args.min_threshold = (g_args.min_threshold == -1 || g_args.min_threshold < 0 || g_args.min_threshold >= 1) ? 0.03: g_args.min_threshold;</div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  g_args.min_qual = (g_args.min_qual == 255) ? 20 : g_args.min_qual;</div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  res = call_variants_from_plup(std::cin, g_args.prefix, g_args.min_qual, g_args.min_threshold);</div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (cmd.compare(<span class="stringliteral">"consensus"</span>) == 0){</div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  opt = getopt( argc, argv, consensus_opt_str);</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  g_args.min_threshold = 0;</div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keywordflow">while</span>( opt != -1 ) {</div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <span class="keywordflow">switch</span>( opt ) {</div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keywordflow">case</span> <span class="charliteral">'t'</span>:</div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  g_args.min_threshold = atof(optarg);</div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <span class="keywordflow">case</span> <span class="charliteral">'p'</span>:</div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  g_args.prefix = optarg;</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keywordflow">case</span> <span class="charliteral">'q'</span>:</div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  g_args.min_qual = atoi(optarg);</div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="keywordflow">case</span> <span class="charliteral">'h'</span>:</div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="keywordflow">case</span> <span class="charliteral">'?'</span>:</div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  print_consensus_usage();</div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  }</div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  opt = getopt( argc, argv, consensus_opt_str);</div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  }</div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <span class="keywordflow">if</span>(g_args.prefix.empty()){</div><div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  print_consensus_usage();</div><div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  }</div><div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  g_args.min_qual = (g_args.min_qual == 255) ? 20 : g_args.min_qual;</div><div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  std::cout <<<span class="stringliteral">"Min Quality"</span> << g_args.min_qual << std::endl;</div><div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  std::cout << <span class="stringliteral">"Threshold: "</span> << g_args.min_threshold << std::endl;</div><div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  res = call_consensus_from_plup(std::cin, g_args.prefix, g_args.min_qual, g_args.min_threshold);</div><div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (cmd.compare(<span class="stringliteral">"removereads"</span>) == 0){</div><div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  opt = getopt( argc, argv, removereads_opt_str);</div><div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <span class="keywordflow">while</span>( opt != -1 ) {</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  <span class="keywordflow">switch</span>( opt ) {</div><div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="keywordflow">case</span> <span class="charliteral">'i'</span>:</div><div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  g_args.bam = optarg;</div><div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="keywordflow">case</span> <span class="charliteral">'p'</span>:</div><div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  g_args.prefix = optarg;</div><div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="keywordflow">case</span> <span class="charliteral">'h'</span>:</div><div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="keywordflow">case</span> <span class="charliteral">'?'</span>:</div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  print_removereads_usage();</div><div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  }</div><div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  opt = getopt( argc, argv, removereads_opt_str);</div><div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  }</div><div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keywordflow">if</span>(optind >= argc){</div><div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  print_removereads_usage();</div><div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  }</div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  uint16_t amp[100];</div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = optind; i<argc;i++){</div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  amp[i] = atoi(argv[i]);</div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  std::cout << amp[i];</div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  }</div><div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="keywordflow">if</span>(g_args.bam.empty() || g_args.prefix.empty()){</div><div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  print_removereads_usage();</div><div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  }</div><div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  res = rmv_reads_from_amplicon(g_args.bam, g_args.region, g_args.prefix, amp, argc - optind);</div><div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span>(cmd.compare(<span class="stringliteral">"filtervariants"</span>) == 0){</div><div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  opt = getopt( argc, argv, filtervariants_opt_str);</div><div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="keywordflow">while</span>( opt != -1 ) {</div><div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="keywordflow">switch</span>( opt ) {</div><div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <span class="keywordflow">case</span> <span class="charliteral">'p'</span>:</div><div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  g_args.prefix = optarg;</div><div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  <span class="keywordflow">case</span> <span class="charliteral">'h'</span>:</div><div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <span class="keywordflow">case</span> <span class="charliteral">'?'</span>:</div><div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  print_filtervariants_usage();</div><div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  }</div><div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  opt = getopt( argc, argv, filtervariants_opt_str);</div><div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  }</div><div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <span class="keywordflow">if</span>(optind >= argc){</div><div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  print_filtervariants_usage();</div><div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  }</div><div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <span class="keywordflow">if</span>(g_args.prefix.empty()){</div><div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  print_filtervariants_usage();</div><div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  }</div><div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  std::string rep = <span class="stringliteral">"get_common_variants.sh "</span>;</div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = optind; i<argc;i++){</div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  rep += argv[i];</div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  rep += <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  }</div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  rep += <span class="stringliteral">" | sort -s -n -k 2 > "</span>+g_args.prefix+<span class="stringliteral">".tsv"</span>;</div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  system(rep.c_str());</div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span>(cmd.compare(<span class="stringliteral">"getmasked"</span>) == 0){</div><div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  opt = getopt( argc, argv, getmasked_opt_str);</div><div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <span class="keywordflow">while</span>( opt != -1 ) {</div><div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keywordflow">switch</span>( opt ) {</div><div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <span class="keywordflow">case</span> <span class="charliteral">'i'</span>:</div><div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  g_args.bam = optarg;</div><div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  <span class="keywordflow">case</span> <span class="charliteral">'b'</span>:</div><div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  g_args.bed = optarg;</div><div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keywordflow">case</span> <span class="charliteral">'h'</span>:</div><div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  <span class="keywordflow">case</span> <span class="charliteral">'?'</span>:</div><div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  print_getmasked_usage();</div><div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  }</div><div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  opt = getopt( argc, argv, getmasked_opt_str);</div><div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  }</div><div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  <span class="keywordflow">if</span>(g_args.bed.empty() || g_args.bam.empty()){</div><div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  print_getmasked_usage();</div><div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  }</div><div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  res = get_primers_with_mismatches(g_args.bed, g_args.bam);</div><div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  } <span class="keywordflow">else</span> <span class="keywordflow">if</span> (cmd.compare(<span class="stringliteral">"trimadapter"</span>) == 0){</div><div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  opt = getopt( argc, argv, trimadapter_opt_str);</div><div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordflow">while</span>( opt != -1 ) {</div><div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <span class="keywordflow">switch</span>( opt ) {</div><div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  <span class="keywordflow">case</span> <span class="charliteral">'1'</span>:</div><div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  g_args.f1 = optarg;</div><div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="keywordflow">case</span> <span class="charliteral">'2'</span>:</div><div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  g_args.f2 = optarg;</div><div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <span class="keywordflow">case</span> <span class="charliteral">'p'</span>:</div><div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  g_args.prefix = optarg;</div><div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <span class="keywordflow">case</span> <span class="charliteral">'a'</span>:</div><div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  g_args.adp_path = optarg;</div><div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  <span class="keywordflow">case</span> <span class="charliteral">'h'</span>:</div><div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  <span class="keywordflow">case</span> <span class="charliteral">'?'</span>:</div><div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  print_trimadapter_usage();</div><div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  }</div><div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  opt = getopt( argc, argv, trimadapter_opt_str);</div><div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  }</div><div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <span class="keywordflow">if</span>(g_args.f1.empty() || g_args.prefix.empty() || g_args.adp_path.empty()){</div><div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  print_trimadapter_usage();</div><div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  }</div><div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  res = trim_adapter(g_args.f1, g_args.f2, g_args.adp_path, g_args.prefix);</div><div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  print_usage();</div><div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  }</div><div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="keywordflow">return</span> res;</div><div class="line"><a name="l00377"></a><span class="lineno"> 377</span> }</div><div class="ttc" id="structargs__t_html"><div class="ttname"><a href="structargs__t.html">args_t</a></div><div class="ttdef"><b>Definition:</b> <a href="ivar_8cpp_source.html#l00015">ivar.cpp:15</a></div></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> <a href="ivar_8cpp_source.html#l00144">ivar.cpp:144</a></div></div>
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