Use functions to convert hits to positions. (a7bf985e) · 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-r430"
		#define CHROMAP_VERSION "0.2.3-r431"

		namespace chromap {

src/hit.h

0 → 100644

+30 −0

Original line number	Diff line number	Diff line
		#ifndef HIT_H_
		#define HIT_H_

		#include "strand.h"

		namespace chromap {

		inline static uint32_t GenerateSequenceIndex(uint64_t seed_hit) {
		return (seed_hit >> 33);
		}

		inline static uint32_t GenerateSequencePosition(uint64_t seed_hit) {
		return (seed_hit >> 1);
		}

		inline static Strand GenerateSequenceStrand(uint64_t seed_hit) {
		if ((seed_hit & 1) == 0) {
		return kPositive;
		}
		return kNegative;
		}

		inline static bool AreTwoHitsOnTheSameStrand(uint64_t seed_hit1,
		uint64_t seed_hit2) {
		return ((seed_hit1 & 1) == (seed_hit2 & 1));
		}

		} // namespace chromap

		#endif // HIT_H_

src/index.cc

+31 −23

Original line number	Diff line number	Diff line
		@@ -5,6 +5,7 @@
		#include <algorithm>
		#include <iostream>

		#include "hit.h"
		#include "minimizer_generator.h"

		namespace chromap {
		@@ -271,21 +272,22 @@ void Index::HeapMergeSeedHitLists(
		}

		uint64_t Index::GenerateCandidatePositionForSingleSeedHit(
		uint64_t reference_seed_hit, uint32_t read_position,
		const Strand &read_strand) const {
		const uint64_t reference_id = reference_seed_hit >> 33;
		const uint32_t reference_position = reference_seed_hit >> 1;
		const Strand reference_strand =
		(reference_seed_hit & 1) == 0 ? kPositive : kNegative;
		uint64_t reference_seed_hit, uint64_t read_seed_hit) const {
		const uint32_t reference_position =
		GenerateSequencePosition(reference_seed_hit);

		const uint32_t read_position = GenerateSequencePosition(read_seed_hit);

		// For now we can't see the reference here. So let us don't validate
		// this seed hit. Instead, we do it later some time when we check the
		// candidates.
		const uint32_t mapping_start_position =
		read_strand == reference_strand
		AreTwoHitsOnTheSameStrand(reference_seed_hit, read_seed_hit)
		? reference_position - read_position
		: reference_position + read_position - kmer_size_ + 1;

		const uint64_t reference_id = GenerateSequenceIndex(reference_seed_hit);

		const uint64_t candidate_position =
		(reference_id << 32) \| mapping_start_position;

		@@ -331,8 +333,9 @@ int Index::CollectSeedHits(int max_seed_frequency,

		const uint64_t reference_seed_hit = kh_value(lookup_table_, khash_iterator);

		const uint32_t read_position = minimizers[mi].GetSequencePosition();
		const Strand read_strand = minimizers[mi].GetSequenceStrand();
		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;
		@@ -340,10 +343,10 @@ int Index::CollectSeedHits(int max_seed_frequency,
		if (is_reference_minimizer_single) {
		const uint64_t candidate_position =
		GenerateCandidatePositionForSingleSeedHit(reference_seed_hit,
		read_position, read_strand);
		read_seed_hit);

		const Strand reference_strand =
		(reference_seed_hit & 1) == 0 ? kPositive : kNegative;
		GenerateSequenceStrand(reference_seed_hit);

		if (read_strand == reference_strand) {
		if (use_heap) {
		@@ -370,12 +373,13 @@ int Index::CollectSeedHits(int max_seed_frequency,
		occurrence_table_[occurrence_offset + oi];

		const uint64_t candidate_position =
		GenerateCandidatePositionForSingleSeedHit(
		reference_seed_hit, read_position, read_strand);
		GenerateCandidatePositionForSingleSeedHit(reference_seed_hit,
		read_seed_hit);

		const uint32_t reference_position = reference_seed_hit >> 1;
		const uint32_t reference_position =
		GenerateSequencePosition(reference_seed_hit);
		const Strand reference_strand =
		(reference_seed_hit & 1) == 0 ? kPositive : kNegative;
		GenerateSequenceStrand(reference_seed_hit);

		if (read_strand == reference_strand) {
		if (use_heap) {
		@@ -521,17 +525,20 @@ int Index::CollectSeedHitsFromRepetitiveReadWithMateInfo(
		}

		const uint64_t reference_seed_hit = kh_value(lookup_table_, khash_iterator);
		const uint32_t read_position = minimizers[mi].GetSequencePosition();
		const Strand read_strand = minimizers[mi].GetSequenceStrand();

		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_id = reference_seed_hit >> 33;
		const uint32_t reference_position = reference_seed_hit >> 1;
		const uint64_t reference_id = GenerateSequenceIndex(reference_seed_hit);
		const uint32_t reference_position =
		GenerateSequencePosition(reference_seed_hit);
		const Strand reference_strand =
		(reference_seed_hit & 1) == 0 ? kPositive : kNegative;
		GenerateSequenceStrand(reference_seed_hit);

		if (read_strand == reference_strand) {
		if (strand == kPositive) {
		@@ -579,10 +586,11 @@ int Index::CollectSeedHitsFromRepetitiveReadWithMateInfo(
		break;
		}

		const uint64_t reference_id = reference_seed_hit >> 33;
		const uint32_t reference_position = reference_seed_hit >> 1;
		const uint64_t reference_id = GenerateSequenceIndex(reference_seed_hit);
		const uint32_t reference_position =
		GenerateSequencePosition(reference_seed_hit);
		const Strand reference_strand =
		(reference_seed_hit & 1) == 0 ? kPositive : kNegative;
		GenerateSequenceStrand(reference_seed_hit);

		if (read_strand == reference_strand) {
		if (strand == kPositive) {

src/index.h

+1 −2

Original line number	Diff line number	Diff line
		@@ -97,8 +97,7 @@ class Index {
		std::vector<uint64_t> &seed_hits) const;

		uint64_t GenerateCandidatePositionForSingleSeedHit(
		uint64_t reference_seed_hit, uint32_t read_position,
		const Strand &read_strand) const;
		uint64_t reference_seed_hit, uint64_t read_seed_hit) const;

		protected:
		int kmer_size_ = 0;

src/minimizer.h

+0 −11

Original line number	Diff line number	Diff line
		@@ -22,17 +22,6 @@ class Minimizer {

		inline uint64_t GetHit() const { return hit_; }

		inline uint32_t GetSequenceIndex() const { return (hit_ >> 33); }

		inline uint32_t GetSequencePosition() const { return (hit_ >> 1); }

		inline Strand GetSequenceStrand() const {
		if ((hit_ & 1) == 0) {
		return kPositive;
		}
		return kNegative;
		}

		inline bool operator<(const Minimizer &m) const {
		if (hash_key_ < m.hash_key_) {
		return true;

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