| 1237 | } |
| 1238 | |
| 1239 | void ChrCopyNumber::deleteFlanks(int telo_centromeric_flanks) { |
| 1240 | int maxRegionLengthToDelete = int(telo_centromeric_flanks/windowSize_); |
| 1241 | for (int i = 0; i < (int)medianValues_.size(); i++) { |
| 1242 | if (medianValues_[i]==NA) { |
| 1243 | if ((i-1>=0)&&(fragmentNotNA_lengths_[i-1]<=maxRegionLengthToDelete)) { |
| 1244 | deleteFragment(i-1); |
| 1245 | for (int j=i-2; j>0; j--) { |
| 1246 | if (fragmentNotNA_lengths_[j]<=maxRegionLengthToDelete) |
| 1247 | deleteFragment(j); |
| 1248 | else |
| 1249 | break; |
| 1250 | } |
| 1251 | } |
| 1252 | if ((i+1<(int)medianValues_.size())&&(fragmentNotNA_lengths_[i+1]<=maxRegionLengthToDelete)) |
| 1253 | deleteFragment(i+1); |
| 1254 | } |
| 1255 | } |
| 1256 | //detele telomeric flanks: |
| 1257 | if (medianValues_[0]!=NA) |
| 1258 | if (fragmentNotNA_lengths_[0]<=maxRegionLengthToDelete) |
| 1259 | deleteFragment(0); |
| 1260 | |
| 1261 | if ((medianValues_[medianValues_.size()-1]!=NA)&&(fragmentNotNA_lengths_[medianValues_.size()-1]<=maxRegionLengthToDelete)) |
| 1262 | deleteFragment(medianValues_.size()-1); |
| 1263 | |
| 1264 | } |
| 1265 | |
| 1266 | |
| 1267 | int ChrCopyNumber::removeLargeExons(float threshold) { |
no outgoing calls
no test coverage detected