| 65 | } |
| 66 | |
| 67 | bool Filter::passLowComplexityFilter(Read* r) { |
| 68 | int diff = 0; |
| 69 | int length = r->length(); |
| 70 | if(length <= 1) |
| 71 | return false; |
| 72 | const char* data = r->mSeq->c_str(); |
| 73 | for(int i=0; i<length-1; i++) { |
| 74 | if(data[i] != data[i+1]) |
| 75 | diff++; |
| 76 | } |
| 77 | if( (double)diff/(double)(length-1) >= mOptions->complexityFilter.threshold ) |
| 78 | return true; |
| 79 | else |
| 80 | return false; |
| 81 | } |
| 82 | |
| 83 | vector<pair<int, int>> Filter::detectLowQualityRegions(Read* r, int windowSize, int quality) { |
| 84 | vector<pair<int, int>> results; |