| 207 | } |
| 208 | |
| 209 | void SNPinGenome::perform(std::string const& mateFile, const std::string& inputFormat, int minimalTotalLetterCountPerPosition, |
| 210 | int minimalQualityPerPosition, bool noisyData,bool CompleteGenomicsData,GenomeCopyNumber& genomeCopyNumber, double breakPointThreshold, |
| 211 | int breakPointType, int minCNAlength, const char* what) |
| 212 | { |
| 213 | if (!pileup_read) { |
| 214 | assignValues(mateFile, inputFormat, minimalTotalLetterCountPerPosition,minimalQualityPerPosition); |
| 215 | } |
| 216 | |
| 217 | if (genomeCopyNumber.ifHasRatio()) { |
| 218 | cout << "..Adding BAF info to the " << what << " dataset" << std::endl; |
| 219 | genomeCopyNumber.addBAFinfo(*this); |
| 220 | cout << "..Recalculate breakpoints using BAF profiles" << std::endl; |
| 221 | genomeCopyNumber.calculateBAFBreakpoints(breakPointThreshold,breakPointType); |
| 222 | cout << "..Recalculate median values" << std::endl; |
| 223 | genomeCopyNumber.calculateCopyNumberMedians(minCNAlength, noisyData, CompleteGenomicsData); |
| 224 | |
| 225 | cout << "..Reannotate copy numbers" << std::endl; |
| 226 | if (genomeCopyNumber.getWESanalysis() == false) |
| 227 | {genomeCopyNumber.calculateCopyNumberProbs_and_genomeLength(breakPointType);} |
| 228 | else |
| 229 | {genomeCopyNumber.calculateCopyNumberProbs_and_exomeLength(breakPointType);} |
| 230 | |
| 231 | } |
| 232 | |
| 233 | cout << "..Done" << std::endl; |
| 234 | } |
| 235 | |
| 236 | long SNPinGenome::processPileUPLine(int & positionCount, char* line, string & oldChr, int & sNPpositionToProceed,int minimalTotalLetterCountPerPosition,int & index, int minimalQualityPerPosition, GenomeCopyNumber* p_genomeCopyNumber) { |
| 237 |
no test coverage detected