Rename a minimizer position as a hit. (4ffcc6aa) · 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-r429"
		#define CHROMAP_VERSION "0.2.3-r430"

		namespace chromap {

src/index.cc

+3 −3

Original line number	Diff line number	Diff line
		@@ -76,7 +76,7 @@ void Index::Construct(uint32_t num_sequences, const SequenceBatch &reference) {
		break;
		}

		occurrence_table_.push_back(minimizers[ti].GetMinimizer());
		occurrence_table_.push_back(minimizers[ti].GetHit());
		previous_key = current_key;
		}

		@@ -225,13 +225,13 @@ void Index::CheckIndex(uint32_t num_sequences,
		uint64_t key = kh_key(lookup_table_, khash_iterator);
		uint64_t value = kh_value(lookup_table_, khash_iterator);
		if (key & 1) { // singleton
		assert(minimizers[i].GetMinimizer() == value);
		assert(minimizers[i].GetHit() == value);
		count = 0;
		} else {
		uint32_t offset = value >> 32;
		uint32_t num_occ = value;
		uint64_t value_in_index = occurrence_table_[offset + count];
		assert(value_in_index == minimizers[i].GetMinimizer());
		assert(value_in_index == minimizers[i].GetHit());
		++count;
		if (count == num_occ) {
		count = 0;

src/minimizer.h

+11 −12

Original line number	Diff line number	Diff line
		@@ -12,23 +12,22 @@ class Minimizer {
		Minimizer() = delete;

		Minimizer(std::pair<uint64_t, uint64_t> minimizer)
		: hash_key_(minimizer.first), minimizer_(minimizer.second) {}
		: hash_key_(minimizer.first), hit_(minimizer.second) {}

		Minimizer(uint64_t hash_key, uint64_t minimizer)
		: hash_key_(hash_key), minimizer_(minimizer) {}
		Minimizer(uint64_t hash_key, uint64_t hit) : hash_key_(hash_key), hit_(hit) {}

		~Minimizer() = default;

		inline uint64_t GetHashKey() const { return hash_key_; }

		inline uint64_t GetMinimizer() const { return minimizer_; }
		inline uint64_t GetHit() const { return hit_; }

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

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

		inline Strand GetSequenceStrand() const {
		if ((minimizer_ & 1) == 0) {
		if ((hit_ & 1) == 0) {
		return kPositive;
		}
		return kNegative;
		@@ -39,7 +38,7 @@ class Minimizer {
		return true;
		}

		if (hash_key_ == m.hash_key_ && minimizer_ < m.minimizer_) {
		if (hash_key_ == m.hash_key_ && hit_ < m.hit_) {
		return true;
		}

		@@ -50,10 +49,10 @@ class Minimizer {
		// The hash value of the kmer.
		uint64_t hash_key_ = 0;

		// The high 31 bits save the reference sequence index in the reference
		// sequence batch. The following 32 bits save the reference position on that
		// sequence. And the lowest bit encodes the strand (0 for positive).
		uint64_t minimizer_ = 0;
		// The high 31 bits save the sequence index in the sequence batch. The
		// following 32 bits save the end position on that sequence. And the lowest
		// bit encodes the strand (0 for positive).
		uint64_t hit_ = 0;
		};

		} // namespace chromap

src/mmcache.hpp

+3 −3

Original line number	Diff line number	Diff line
		@@ -42,7 +42,7 @@ class mm_cache {
		int direction = 0;
		for (i = 0; i < size; ++i) {
		if (cache.minimizers[i] != minimizers[i].GetHashKey() \|\|
		(minimizers[i].GetMinimizer() & 1) != cache.strands[i])
		(minimizers[i].GetHit() & 1) != cache.strands[i])
		break;
		}
		if (i >= size) {
		@@ -58,7 +58,7 @@ class mm_cache {

		for (i = 0, j = size - 1; i < size; ++i, --j) {
		if (cache.minimizers[i] != minimizers[j].GetHashKey() \|\|
		(minimizers[j].GetMinimizer() & 1) == cache.strands[i])
		(minimizers[j].GetHit() & 1) == cache.strands[i])
		break;
		}
		if (i >= size) {
		@@ -263,7 +263,7 @@ if (cache[hidx].finger_print_cnt_sum <= 5)
		cache[hidx].strands.resize(msize);
		for (i = 0; i < msize; ++i) {
		cache[hidx].minimizers[i] = minimizers[i].GetHashKey();
		cache[hidx].strands[i] = (minimizers[i].GetMinimizer() & 1);
		cache[hidx].strands[i] = (minimizers[i].GetHit() & 1);
		}
		for (i = 0; i < msize - 1; ++i) {
		cache[hidx].offsets[i] =

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