| 150 | typedef vector<Alignment> AlignmentVector; |
| 151 | |
| 152 | static void readAlignment(string& line, string& readID, |
| 153 | Sequence& seq, AlignmentVector& alignments) |
| 154 | { |
| 155 | char anchor; |
| 156 | istringstream s(line); |
| 157 | |
| 158 | if (opt::colourSpace || opt::csToNt) |
| 159 | s >> readID >> anchor >> seq; |
| 160 | else |
| 161 | s >> readID >> seq; |
| 162 | |
| 163 | Alignment alignment; |
| 164 | while (s >> alignment) |
| 165 | alignments.push_back(alignment); |
| 166 | |
| 167 | if (!alignments.empty() && opt::csToNt |
| 168 | && seq.find_first_not_of("0123") == string::npos) |
| 169 | seq = colourToNucleotideSpace(anchor, seq); |
| 170 | } |
| 171 | |
| 172 | /** Builds the pile up of all reads based on the alignments and |
| 173 | * read sequence */ |
no test coverage detected