Rename some variables and remove unused variables. (bcb3bd05) · 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-r432"
		#define CHROMAP_VERSION "0.2.3-r433"

		namespace chromap {

src/index.cc

+11 −13

Original line number	Diff line number	Diff line
		@@ -331,24 +331,20 @@ int Index::CollectSeedHits(int max_seed_frequency,
		continue;
		}

		const uint64_t reference_seed_hit = kh_value(lookup_table_, khash_iterator);

		const uint64_t read_seed_hit = minimizers[mi].GetHit();
		const uint32_t read_position = GenerateSequencePosition(read_seed_hit);
		const Strand read_strand = GenerateSequenceStrand(read_seed_hit);

		const bool is_reference_minimizer_single =
		(kh_key(lookup_table_, khash_iterator) & 1) > 0;

		if (is_reference_minimizer_single) {
		const uint64_t reference_seed_hit =
		kh_value(lookup_table_, khash_iterator);

		const uint64_t candidate_position =
		GenerateCandidatePositionForSingleSeedHit(reference_seed_hit,
		read_seed_hit);

		const Strand reference_strand =
		GenerateSequenceStrand(reference_seed_hit);

		if (read_strand == reference_strand) {
		if (AreTwoHitsOnTheSameStrand(reference_seed_hit, read_seed_hit)) {
		if (use_heap) {
		positive_hit_lists[mi].push_back(candidate_position);
		} else {
		@@ -364,8 +360,12 @@ int Index::CollectSeedHits(int max_seed_frequency,
		continue;
		}

		const uint32_t occurrence_offset = reference_seed_hit >> 32;
		const uint32_t num_occurrences = reference_seed_hit;
		const uint32_t read_position = GenerateSequencePosition(read_seed_hit);

		const uint64_t occurrence_info = kh_value(lookup_table_, khash_iterator);

		const uint32_t occurrence_offset = occurrence_info >> 32;
		const uint32_t num_occurrences = occurrence_info;

		if (num_occurrences < (uint32_t)max_seed_frequency) {
		for (uint32_t oi = 0; oi < num_occurrences; ++oi) {
		@@ -378,10 +378,8 @@ int Index::CollectSeedHits(int max_seed_frequency,

		const uint32_t reference_position =
		GenerateSequencePosition(reference_seed_hit);
		const Strand reference_strand =
		GenerateSequenceStrand(reference_seed_hit);

		if (read_strand == reference_strand) {
		if (AreTwoHitsOnTheSameStrand(reference_seed_hit, read_seed_hit)) {
		if (use_heap) {
		if (reference_position < read_position) {
		is_candidate_position_list_sorted = false;

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