Shorter func name. (7cd04fb4) · 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-r447"
		#define CHROMAP_VERSION "0.2.3-r448"

		namespace chromap {

src/index.cc

+7 −10

Original line number	Diff line number	Diff line
		@@ -38,8 +38,7 @@ void Index::Construct(uint32_t num_sequences, const SequenceBatch &reference) {

		occurrence_table_.reserve(num_minimizers);

		uint64_t previous_key =
		GenerateHashKeyInLookupTable(minimizers[0].GetHashKey());
		uint64_t previous_key = GenerateHashInLookupTable(minimizers[0].GetHash());
		uint32_t num_previous_minimizer_occurrences = 0;
		uint64_t num_nonsingletons = 0;
		uint32_t num_singletons = 0;
		@@ -47,9 +46,8 @@ void Index::Construct(uint32_t num_sequences, const SequenceBatch &reference) {
		for (uint32_t ti = 0; ti <= num_minimizers; ++ti) {
		const bool is_last_iteration = ti == num_minimizers;
		const uint64_t current_key =
		is_last_iteration
		? previous_key + 1
		: GenerateHashKeyInLookupTable(minimizers[ti].GetHashKey());
		is_last_iteration ? previous_key + 1
		: GenerateHashInLookupTable(minimizers[ti].GetHash());

		if (current_key != previous_key) {
		int khash_return_code = 0;
		@@ -223,9 +221,8 @@ void Index::CheckIndex(uint32_t num_sequences,

		uint32_t count = 0;
		for (uint32_t i = 0; i < minimizers.size(); ++i) {
		khiter_t khash_iterator =
		kh_get(k64, lookup_table_,
		GenerateHashKeyInLookupTable(minimizers[i].GetHashKey()));
		khiter_t khash_iterator = kh_get(
		k64, lookup_table_, GenerateHashInLookupTable(minimizers[i].GetHash()));
		assert(khash_iterator != kh_end(lookup_table_));
		uint64_t key = kh_key(lookup_table_, khash_iterator);
		uint64_t value = kh_value(lookup_table_, khash_iterator);
		@@ -283,7 +280,7 @@ int Index::GenerateCandidatePositions(
		for (uint32_t mi = 0; mi < num_minimizers; ++mi) {
		khiter_t khash_iterator =
		kh_get(k64, lookup_table_,
		GenerateHashKeyInLookupTable(minimizers[mi].GetHashKey()));
		GenerateHashInLookupTable(minimizers[mi].GetHash()));
		if (khash_iterator == kh_end(lookup_table_)) {
		// std::cerr << "The minimizer is not in reference!\n";
		continue;
		@@ -484,7 +481,7 @@ int Index::GenerateCandidatePositionsFromRepetitiveReadWithMateInfoOnOneStrand(
		for (uint32_t mi = 0; mi < minimizers.size(); ++mi) {
		khiter_t khash_iterator =
		kh_get(k64, lookup_table_,
		GenerateHashKeyInLookupTable(minimizers[mi].GetHashKey()));
		GenerateHashInLookupTable(minimizers[mi].GetHash()));
		if (khash_iterator == kh_end(lookup_table_)) {
		// std::cerr << "The minimizer is not in reference!\n";
		continue;

src/index_utils.h

+2 −3

Original line number	Diff line number	Diff line
		@@ -16,9 +16,8 @@ KHASH_INIT(/name=/k64, /khkey_t=/uint64_t, /khval_t=/uint64_t,

		namespace chromap {

		inline static uint64_t GenerateHashKeyInLookupTable(
		uint64_t minimizer_hash_key) {
		return minimizer_hash_key << 1;
		inline static uint64_t GenerateHashInLookupTable(uint64_t minimizer_hash) {
		return minimizer_hash << 1;
		}

		inline static uint64_t GenerateEntryValueInLookupTable(

src/minimizer.h

+7 −7

Original line number	Diff line number	Diff line
		@@ -13,13 +13,13 @@ class Minimizer {
		Minimizer() = delete;

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

		Minimizer(uint64_t hash_key, uint64_t hit) : hash_key_(hash_key), hit_(hit) {}
		Minimizer(uint64_t hash, uint64_t hit) : hash_(hash), hit_(hit) {}

		~Minimizer() = default;

		inline uint64_t GetHashKey() const { return hash_key_; }
		inline uint64_t GetHash() const { return hash_; }

		inline uint64_t GetHit() const { return hit_; }

		@@ -36,11 +36,11 @@ class Minimizer {
		}

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

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

		@@ -48,8 +48,8 @@ class Minimizer {
		}

		private:
		// The hash value of the kmer.
		uint64_t hash_key_ = 0;
		// The hash of the kmer.
		uint64_t hash_ = 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

src/mmcache.hpp

+14 −14

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

		for (i = 0, j = size - 1; i < size; ++i, --j) {
		if (cache.minimizers[i] != minimizers[j].GetHashKey() \|\|
		if (cache.minimizers[i] != minimizers[j].GetHash() \|\|
		(minimizers[j].GetHit() & 1) == cache.strands[i])
		break;
		}
		@@ -114,16 +114,16 @@ class mm_cache {
		int i;
		int msize = minimizers.size();
		if (msize == 0) return -1;
		if ((head_mm[(minimizers[0].GetHashKey() >> 6) & HEAD_MM_ARRAY_MASK] &
		(1ull << (minimizers[0].GetHashKey() & 0x3f))) == 0)
		if ((head_mm[(minimizers[0].GetHash() >> 6) & HEAD_MM_ARRAY_MASK] &
		(1ull << (minimizers[0].GetHash() & 0x3f))) == 0)
		return -1;
		uint64_t h = 0;
		// for (i = 0 ; i < msize; ++i)
		// h += (minimizers[i].first);
		if (msize == 1) {
		h = (minimizers[0].GetHashKey());
		h = (minimizers[0].GetHash());
		} else {
		h = minimizers[0].GetHashKey() + minimizers[msize - 1].GetHashKey();
		h = minimizers[0].GetHash() + minimizers[msize - 1].GetHash();
		}

		int hidx = h % cache_size;
		@@ -187,10 +187,10 @@ class mm_cache {
		if (msize == 0)
		return;
		else if (msize == 1) {
		h = f = (minimizers[0].GetHashKey());
		h = f = (minimizers[0].GetHash());
		} else {
		h = minimizers[0].GetHashKey() + minimizers[msize - 1].GetHashKey();
		f = minimizers[0].GetHashKey() ^ minimizers[msize - 1].GetHashKey();
		h = minimizers[0].GetHash() + minimizers[msize - 1].GetHash();
		f = minimizers[0].GetHash() ^ minimizers[msize - 1].GetHash();
		}
		int hidx = h % cache_size;
		int finger_print = f % FINGER_PRINT_SIZE;
		@@ -263,7 +263,7 @@ if (cache[hidx].finger_print_cnt_sum <= 5)
		cache[hidx].offsets.resize(msize - 1);
		cache[hidx].strands.resize(msize);
		for (i = 0; i < msize; ++i) {
		cache[hidx].minimizers[i] = minimizers[i].GetHashKey();
		cache[hidx].minimizers[i] = minimizers[i].GetHash();
		cache[hidx].strands[i] = (minimizers[i].GetHit() & 1);
		}
		for (i = 0; i < msize - 1; ++i) {
		@@ -286,10 +286,10 @@ if (cache[hidx].finger_print_cnt_sum <= 5)
		cache[hidx].negative_candidates[i].position -= shift;

		// Update head mm array
		head_mm[(minimizers[0].GetHashKey() >> 6) & HEAD_MM_ARRAY_MASK] \|=
		(1ull << (minimizers[0].GetHashKey() & 0x3f));
		head_mm[(minimizers[msize - 1].GetHashKey() >> 6) & HEAD_MM_ARRAY_MASK] \|=
		(1ull << (minimizers[msize - 1].GetHashKey() & 0x3f));
		head_mm[(minimizers[0].GetHash() >> 6) & HEAD_MM_ARRAY_MASK] \|=
		(1ull << (minimizers[0].GetHash() & 0x3f));
		head_mm[(minimizers[msize - 1].GetHash() >> 6) & HEAD_MM_ARRAY_MASK] \|=
		(1ull << (minimizers[msize - 1].GetHash() & 0x3f));
		}
		}

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