| 163 | } |
| 164 | |
| 165 | static void |
| 166 | doReadIntegrity(const ReadAlignMap::value_type& a) |
| 167 | { |
| 168 | AlignmentVector::const_iterator refAlignIter = a.second.begin(); |
| 169 | unsigned firstStart, lastEnd, largestSize; |
| 170 | Alignment first, last, largest; |
| 171 | |
| 172 | firstStart = refAlignIter->read_start_pos; |
| 173 | lastEnd = firstStart + refAlignIter->align_length; |
| 174 | largestSize = refAlignIter->align_length; |
| 175 | first = last = largest = *refAlignIter; |
| 176 | ++refAlignIter; |
| 177 | |
| 178 | // for each alignment in the vector a.second |
| 179 | for (; refAlignIter != a.second.end(); ++refAlignIter) { |
| 180 | if ((unsigned)refAlignIter->read_start_pos < firstStart) { |
| 181 | firstStart = refAlignIter->read_start_pos; |
| 182 | first = *refAlignIter; |
| 183 | } |
| 184 | if ((unsigned)(refAlignIter->read_start_pos + refAlignIter->align_length) > lastEnd) { |
| 185 | lastEnd = refAlignIter->read_start_pos + refAlignIter->align_length; |
| 186 | last = *refAlignIter; |
| 187 | } |
| 188 | if ((unsigned)refAlignIter->align_length > largestSize) { |
| 189 | largestSize = refAlignIter->align_length; |
| 190 | largest = *refAlignIter; |
| 191 | } |
| 192 | } |
| 193 | |
| 194 | if (largest.contig != last.contig) { |
| 195 | Estimate est; |
| 196 | unsigned largest_end = largest.read_start_pos + largest.align_length - opt::k; |
| 197 | int distance = last.read_start_pos - largest_end; |
| 198 | est.first = find_vertex(last.contig, largest.isRC != last.isRC, g_contigNames); |
| 199 | est.second.distance = distance - opt::k; |
| 200 | est.second.numPairs = 1; |
| 201 | est.second.stdDev = 0; |
| 202 | addEstimate(estMap, largest, est, false); |
| 203 | } |
| 204 | |
| 205 | if (largest.contig != first.contig && largest.contig != last.contig) { |
| 206 | Estimate est; |
| 207 | unsigned first_end = first.read_start_pos + first.align_length - opt::k; |
| 208 | int distance = last.read_start_pos - first_end; |
| 209 | est.first = find_vertex(last.contig, first.isRC != last.isRC, g_contigNames); |
| 210 | est.second.distance = distance - opt::k; |
| 211 | est.second.numPairs = 1; |
| 212 | est.second.stdDev = 0; |
| 213 | addEstimate(estMap, first, est, false); |
| 214 | } |
| 215 | |
| 216 | if (largest.contig != first.contig) { |
| 217 | largest.flipQuery(); |
| 218 | first.flipQuery(); |
| 219 | Estimate est; |
| 220 | unsigned largest_end = largest.read_start_pos + largest.align_length - opt::k; |
| 221 | int distance = first.read_start_pos - largest_end; |
| 222 | est.first = find_vertex(first.contig, largest.isRC != first.isRC, g_contigNames); |
no test coverage detected