Avoid passing too many parameters. (0ec61ada) · Commits · github_fork / Chromap

src/mapping_generator.h

+272 −356

File changed.

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+33 −0

Original line number	Diff line number	Diff line
		@@ -60,6 +60,39 @@ class PairedEndMappingMetadata {
		return num_second_best_mappings_;
		}

		// TODO: think how to deal with the code copy.
		inline const std::vector<std::pair<uint32_t, uint32_t>> &GetBestMappings(
		Direction first_mapping_direction,
		Direction second_mapping_direction) const {
		if (first_mapping_direction == kPositive) {
		if (second_mapping_direction == kPositive) {
		return F1F2_best_mappings_;
		}
		return F1R2_best_mappings_;
		} else {
		if (second_mapping_direction == kPositive) {
		return F2R1_best_mappings_;
		}
		return R1R2_best_mappings_;
		}
		}

		inline std::vector<std::pair<uint32_t, uint32_t>> &GetBestMappings(
		Direction first_mapping_direction,
		Direction second_mapping_direction) {
		if (first_mapping_direction == kPositive) {
		if (second_mapping_direction == kPositive) {
		return F1F2_best_mappings_;
		}
		return F1R2_best_mappings_;
		} else {
		if (second_mapping_direction == kPositive) {
		return F2R1_best_mappings_;
		}
		return R1R2_best_mappings_;
		}
		}

		inline void SetMinSumErrors(int min_sum_errors) {
		min_sum_errors_ = min_sum_errors;
		}