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root/gclib/tophat_cpp/inserts.cpp
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# Line 154 | Line 154
154            
155            if (h1.insert_id() == h2.insert_id())
156              {
157 <              // max mate inner distance (genomic)
158 <              int min_mate_inner_dist = inner_dist_mean - inner_dist_std_dev;
159 <              if (max_mate_inner_dist == -1)
160 <                {
161 <                  max_mate_inner_dist = inner_dist_mean + inner_dist_std_dev;
162 <                }
163 <              
164 <              InsertAlignmentGrade s(h1, h2, min_mate_inner_dist, max_mate_inner_dist);
157 >              InsertAlignmentGrade s(h1, h2);
158                
159                pair<InsertAlignmentGrade, vector<InsertAlignment> >& insert_best
160                  = best_status_for_inserts[obs_order];

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