Func to validate candidate position range. (411e025a) · Commits · github_fork / Chromap

src/chromap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@
		#include "temp_mapping.h"
		#include "utils.h"

		#define CHROMAP_VERSION "0.2.3-r408"
		#define CHROMAP_VERSION "0.2.3-r409"

		namespace chromap {

src/mapping_generator.h

+30 −21

Original line number	Diff line number	Diff line
		@@ -61,6 +61,9 @@ class MappingGenerator {
		std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs);

		private:
		bool IsValidCandidate(uint32_t rid, uint32_t position, uint32_t read_length,
		const SequenceBatch &reference);

		bool DirectlyGenerateOneNonSplitMappingSupportedByAllMinimizers(
		const SequenceBatch &read_batch, uint32_t read_index,
		const SequenceBatch &reference, MappingMetadata &mapping_metadata);
		@@ -193,6 +196,25 @@ void MappingGenerator<MappingRecord>::VerifyCandidates(
		}
		}

		// Return true if the candidate position is valid on the reference with rid.
		// Note only the position is checked and the input rid is not checked in this
		// function. So the input rid must be valid.
		template <typename MappingRecord>
		bool MappingGenerator<MappingRecord>::IsValidCandidate(
		uint32_t rid, uint32_t position, uint32_t read_length,
		const SequenceBatch &reference) {
		const uint32_t reference_length = reference.GetSequenceLengthAt(rid);

		if (position < (uint32_t)mapping_parameters_.error_threshold \|\|
		position >= reference_length \|\|
		position + read_length + mapping_parameters_.error_threshold >=
		reference_length) {
		return false;
		}

		return true;
		}

		// Return true when there is one non-split mapping generated and the mapping is
		// supported by all the minimizers.
		template <typename MappingRecord>
		@@ -275,14 +297,8 @@ bool MappingGenerator<MappingRecord>::
		read_length + 1;
		}

		bool is_valid_candidate = true;
		if (position < (uint32_t)mapping_parameters_.error_threshold \|\|
		position >= reference.GetSequenceLengthAt(rid) \|\|
		position + read_length + mapping_parameters_.error_threshold >=
		reference.GetSequenceLengthAt(rid)) {
		is_valid_candidate = false;
		}

		const bool is_valid_candidate =
		IsValidCandidate(rid, position, read_length, reference);
		if (is_valid_candidate) {
		if (all_minimizer_candidate_direction == kPositive) {
		positive_mappings.emplace_back(
		@@ -332,11 +348,8 @@ void MappingGenerator<MappingRecord>::VerifyCandidatesOnOneDirectionUsingSIMD(
		if (candidate_direction == kNegative) {
		position = position - read_length + 1;
		}
		if (position < (uint32_t)mapping_parameters_.error_threshold \|\|
		position >= reference.GetSequenceLengthAt(rid) \|\|
		position + read_length + mapping_parameters_.error_threshold >=
		reference.GetSequenceLengthAt(rid)) {
		// not a valid candidate

		if (!IsValidCandidate(rid, position, read_length, reference)) {
		++candidate_index;
		continue;
		} else {
		@@ -458,12 +471,11 @@ void MappingGenerator<MappingRecord>::VerifyCandidatesOnOneDirectionUsingSIMD(
		if (candidate_direction == kNegative) {
		position = position - read_length + 1;
		}
		if (position < (uint32_t)mapping_parameters_.error_threshold \|\|
		position >= reference.GetSequenceLengthAt(rid) \|\|
		position + read_length + mapping_parameters_.error_threshold >=
		reference.GetSequenceLengthAt(rid)) {

		if (!IsValidCandidate(rid, position, read_length, reference)) {
		continue;
		}

		int mapping_end_position;
		int num_errors;
		if (candidate_direction == kPositive) {
		@@ -542,10 +554,7 @@ void MappingGenerator<MappingRecord>::VerifyCandidatesOnOneDirection(
		position = position - read_length + 1;
		}

		if (position < (uint32_t)mapping_parameters_.error_threshold \|\|
		position >= reference.GetSequenceLengthAt(rid) \|\|
		position + read_length + mapping_parameters_.error_threshold >=
		reference.GetSequenceLengthAt(rid)) {
		if (!IsValidCandidate(rid, position, read_length, reference)) {
		continue;
		}

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