| 4177 | return 0; |
| 4178 | } |
| 4179 | float GenomeCopyNumber::removeLargeExons(float iqrToKeep) { |
| 4180 | float maxLength = 0; |
| 4181 | vector<ChrCopyNumber>::iterator it; |
| 4182 | int totalNumberExons=0; |
| 4183 | float numberOfRemovedExons = 0; |
| 4184 | vector <float> exonLengths; |
| 4185 | |
| 4186 | for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { |
| 4187 | for (int i=0; i < it->getLength(); i++) { |
| 4188 | exonLengths.push_back(it->getEndAtBin(i)-it->getCoordinateAtBin(i)); |
| 4189 | totalNumberExons++; |
| 4190 | } |
| 4191 | } |
| 4192 | maxLength=get_iqr(exonLengths)/2*iqrToKeep+get_median(exonLengths); |
| 4193 | |
| 4194 | for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) { |
| 4195 | numberOfRemovedExons+=it->removeLargeExons(maxLength); |
| 4196 | } |
| 4197 | return numberOfRemovedExons/totalNumberExons; |
| 4198 | } |
| 4199 | int GenomeCopyNumber::focusOnCapture (std::string const& captureFile) { |
| 4200 | ifstream file (captureFile.c_str()); |
| 4201 | string line; |
nothing calls this directly
no test coverage detected