| 49 | } |
| 50 | |
| 51 | void |
| 52 | QCSpacedSeedsPatterns(const std::vector<std::string>& patterns) |
| 53 | { |
| 54 | int k = patterns[0].size(); |
| 55 | |
| 56 | for (const auto& pattern : patterns) { |
| 57 | int patternBasesCovered = k; |
| 58 | bool hasZero = false; |
| 59 | for (const char c : pattern) { |
| 60 | if (c == '0') { |
| 61 | hasZero = true; |
| 62 | patternBasesCovered--; |
| 63 | break; |
| 64 | } |
| 65 | } |
| 66 | if (opt::verbose && !hasZero) { |
| 67 | std::cerr << "A spaced seed has no zeros!\n"; |
| 68 | } |
| 69 | if (opt::verbose && (patternBasesCovered < k * SPACED_SEEDS_QC_MIN_BASES_PATTERN)) { |
| 70 | std::cerr << "A spaced seed pattern does not cover enough bases!\n"; |
| 71 | } |
| 72 | } |
| 73 | |
| 74 | const auto combinations = genCombinations(SPACED_SEEDS_COUNT, SPACED_SEEDS_MIN_HITS); |
| 75 | std::string overallErrorCoverage(k, '1'); |
| 76 | int overallErrorsCovered = 0; |
| 77 | std::string overall_base_coverage(k, '0'); |
| 78 | int overallBasesCovered = 0; |
| 79 | std::string worstCombinationCoverage(k, '1'); |
| 80 | int worstCombinationBasesCovered = k; |
| 81 | |
| 82 | for (auto combination : combinations) { |
| 83 | std::string combinationCoverage(k, '0'); |
| 84 | int combinationBasesCovered = 0; |
| 85 | for (auto index : combination) { |
| 86 | const auto& pattern = patterns[index]; |
| 87 | for (unsigned i = 0; i < pattern.size(); i++) { |
| 88 | if (pattern[i] == '1' && combinationCoverage[i] != '1') { |
| 89 | combinationCoverage[i] = '1'; |
| 90 | combinationBasesCovered++; |
| 91 | } |
| 92 | } |
| 93 | } |
| 94 | if (combinationBasesCovered < worstCombinationBasesCovered) { |
| 95 | worstCombinationCoverage = combinationCoverage; |
| 96 | worstCombinationBasesCovered = combinationBasesCovered; |
| 97 | } |
| 98 | if (opt::verbose && (combinationBasesCovered < |
| 99 | combinationCoverage.size() * SPACED_SEEDS_QC_MIN_BASES_COMBINATION)) { |
| 100 | std::cerr << "A spaced seed combination does not cover enough bases!\n"; |
| 101 | } |
| 102 | |
| 103 | for (unsigned i = 0; i < combinationCoverage.size(); i++) { |
| 104 | if (combinationCoverage[i] == '0') { |
| 105 | if (overallErrorCoverage[i] != '0') { |
| 106 | overallErrorCoverage[i] = '0'; |
| 107 | overallErrorsCovered++; |
| 108 | } |
no test coverage detected