| 701 | } |
| 702 | |
| 703 | int ChrCopyNumber::getCoveredPart(int breakPointStart, int breakPointEnd) { //for exome-seq: get length of the genome covered by the targeted region (from breakPointStart to breakPointEnd) |
| 704 | int lengthCovered = 0; |
| 705 | for (int i = breakPointStart; i<=breakPointEnd; i++) { |
| 706 | lengthCovered+=ends_[i]-coordinates_[i]+1; |
| 707 | } |
| 708 | return lengthCovered; |
| 709 | } |
| 710 | |
| 711 | void ChrCopyNumber::calculateCopyNumberMedian(int ploidy, int minCNAlength, bool noisyData, bool CompleteGenomicsData, bool isLogged){ //create median profiles using 'bpfinal_' and store them in medianProfile_, info about medians themselves is stored in medianValues_ and about SD in sd_, lengths of fragments in bpLengths_ |
| 712 | if (ploidy!=ploidy_) { |
nothing calls this directly
no outgoing calls
no test coverage detected