Rename seed hit lists. (69e2b61f) · Commits · github_fork / Chromap

src/chromap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@
		#include "temp_mapping.h"
		#include "utils.h"

		#define CHROMAP_VERSION "0.2.3-r431"
		#define CHROMAP_VERSION "0.2.3-r432"

		namespace chromap {

src/index.cc

+11 −11

Original line number	Diff line number	Diff line
		@@ -303,13 +303,13 @@ int Index::CollectSeedHits(int max_seed_frequency,
		bool use_heap) const {
		const uint32_t num_minimizers = minimizers.size();

		std::vector<std::vector<uint64_t>> mm_positive_hits;
		std::vector<std::vector<uint64_t>> mm_negative_hits;
		std::vector<std::vector<uint64_t>> positive_hit_lists;
		std::vector<std::vector<uint64_t>> negative_hit_lists;

		if (use_heap) {
		for (uint32_t i = 0; i < num_minimizers; ++i) {
		mm_positive_hits.emplace_back(std::vector<uint64_t>());
		mm_negative_hits.emplace_back(std::vector<uint64_t>());
		positive_hit_lists.emplace_back(std::vector<uint64_t>());
		negative_hit_lists.emplace_back(std::vector<uint64_t>());
		}
		}

		@@ -350,13 +350,13 @@ int Index::CollectSeedHits(int max_seed_frequency,

		if (read_strand == reference_strand) {
		if (use_heap) {
		mm_positive_hits[mi].push_back(candidate_position);
		positive_hit_lists[mi].push_back(candidate_position);
		} else {
		positive_hits.push_back(candidate_position);
		}
		} else {
		if (use_heap) {
		mm_negative_hits[mi].push_back(candidate_position);
		negative_hit_lists[mi].push_back(candidate_position);
		} else {
		negative_hits.push_back(candidate_position);
		}
		@@ -386,13 +386,13 @@ int Index::CollectSeedHits(int max_seed_frequency,
		if (reference_position < read_position) {
		is_candidate_position_list_sorted = false;
		}
		mm_positive_hits[mi].push_back(candidate_position);
		positive_hit_lists[mi].push_back(candidate_position);
		} else {
		positive_hits.push_back(candidate_position);
		}
		} else {
		if (use_heap) {
		mm_negative_hits[mi].push_back(candidate_position);
		negative_hit_lists[mi].push_back(candidate_position);
		} else {
		negative_hits.push_back(candidate_position);
		}
		@@ -422,11 +422,11 @@ int Index::CollectSeedHits(int max_seed_frequency,
		// TODO: try to remove this sorting.
		if (!is_candidate_position_list_sorted) {
		for (uint32_t mi = 0; mi < num_minimizers; ++mi) {
		std::sort(mm_positive_hits[mi].begin(), mm_positive_hits[mi].end());
		std::sort(positive_hit_lists[mi].begin(), positive_hit_lists[mi].end());
		}
		}
		HeapMergeSeedHitLists(mm_positive_hits, positive_hits);
		HeapMergeSeedHitLists(mm_negative_hits, negative_hits);
		HeapMergeSeedHitLists(positive_hit_lists, positive_hits);
		HeapMergeSeedHitLists(negative_hit_lists, negative_hits);
		} else {
		std::sort(positive_hits.begin(), positive_hits.end());
		std::sort(negative_hits.begin(), negative_hits.end());

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