Use encapsulated Minimizer funcs. (6eb7b958) · Commits · github_fork / Chromap

src/mmcache.hpp

+12 −15

Original line number	Original line	Diff line number	Diff line
	@@ -48,9 +48,8 @@ class mm_cache {
	}		}
	if (i >= size) {		if (i >= size) {
	for (i = 0; i < size - 1; ++i) {		for (i = 0; i < size - 1; ++i) {
	if (cache.offsets[i] !=		if (cache.offsets[i] != ((int)minimizers[i + 1].GetSequencePosition() -
	((int)GenerateSequencePosition(minimizers[i + 1].GetHit()) -		(int)minimizers[i].GetSequencePosition()))
	(int)GenerateSequencePosition(minimizers[i].GetHit())))
	break;		break;
	}		}
	if (i >= size - 1) direction = 1;		if (i >= size - 1) direction = 1;
	@@ -66,8 +65,8 @@ class mm_cache {
	if (i >= size) {		if (i >= size) {
	for (i = 0, j = size - 1; i < size - 1; ++i, --j) {		for (i = 0, j = size - 1; i < size - 1; ++i, --j) {
	if (cache.offsets[i] !=		if (cache.offsets[i] !=
	((int)GenerateSequencePosition(minimizers[j].GetHit())) -		((int)minimizers[j].GetSequencePosition()) -
	((int)GenerateSequencePosition(minimizers[j - 1].GetHit())))		((int)minimizers[j - 1].GetSequencePosition()))
	break;		break;
	}		}

	@@ -134,7 +133,7 @@ class mm_cache {
	neg_candidates = cache[hidx].negative_candidates;		neg_candidates = cache[hidx].negative_candidates;
	repetitive_seed_length = cache[hidx].repetitive_seed_length;		repetitive_seed_length = cache[hidx].repetitive_seed_length;
	int size = pos_candidates.size();		int size = pos_candidates.size();
	int shift = (int)GenerateSequencePosition(minimizers[0].GetHit());		int shift = (int)minimizers[0].GetSequencePosition();
	for (i = 0; i < size; ++i) {		for (i = 0; i < size; ++i) {
	uint64_t rid = pos_candidates[i].position >> 32;		uint64_t rid = pos_candidates[i].position >> 32;
	int rpos = (int)pos_candidates[i].position;		int rpos = (int)pos_candidates[i].position;
	@@ -148,9 +147,8 @@ class mm_cache {
	int size = cache[hidx].negative_candidates.size();		int size = cache[hidx].negative_candidates.size();
	// Start position of the last minimizer shoud equal the first minimizer's		// Start position of the last minimizer shoud equal the first minimizer's
	// end position in rc "read".		// end position in rc "read".
	int shift =		int shift = read_len -
	read_len -		((int)minimizers[msize - 1].GetSequencePosition()) - 1 +
	((int)GenerateSequencePosition(minimizers[msize - 1].GetHit())) - 1 +
	kmer_length - 1;		kmer_length - 1;

	pos_candidates = cache[hidx].negative_candidates;		pos_candidates = cache[hidx].negative_candidates;
	@@ -243,7 +241,7 @@ if (cache[hidx].finger_print_cnt_sum <= 5)
	return;		return;
	}		}
	int size = pos_candidates.size();		int size = pos_candidates.size();
	int shift = (int)GenerateSequencePosition(minimizers[0].GetHit());		int shift = (int)minimizers[0].GetSequencePosition();
	// Do not cache if it is too near the start.		// Do not cache if it is too near the start.
	for (i = 0; i < size; ++i)		for (i = 0; i < size; ++i)
	if ((int)pos_candidates[i].position < kmer_length + shift) {		if ((int)pos_candidates[i].position < kmer_length + shift) {
	@@ -255,8 +253,7 @@ if (cache[hidx].finger_print_cnt_sum <= 5)
	size = neg_candidates.size();		size = neg_candidates.size();
	for (i = 0; i < size; ++i)		for (i = 0; i < size; ++i)
	if ((int)neg_candidates[i].position -		if ((int)neg_candidates[i].position -
	((int)GenerateSequencePosition(		((int)minimizers[msize - 1].GetSequencePosition()) <
	minimizers[msize - 1].GetHit())) <
	kmer_length + shift) {		kmer_length + shift) {
	cache[hidx].offsets.clear();		cache[hidx].offsets.clear();
	cache[hidx].strands.clear();		cache[hidx].strands.clear();
	@@ -271,8 +268,8 @@ if (cache[hidx].finger_print_cnt_sum <= 5)
	}		}
	for (i = 0; i < msize - 1; ++i) {		for (i = 0; i < msize - 1; ++i) {
	cache[hidx].offsets[i] =		cache[hidx].offsets[i] =
	((int)GenerateSequencePosition(minimizers[i + 1].GetHit())) -		((int)minimizers[i + 1].GetSequencePosition()) -
	((int)GenerateSequencePosition(minimizers[i].GetHit()));		((int)minimizers[i].GetSequencePosition());
	}		}
	std::vector<Candidate>().swap(cache[hidx].positive_candidates);		std::vector<Candidate>().swap(cache[hidx].positive_candidates);
	std::vector<Candidate>().swap(cache[hidx].negative_candidates);		std::vector<Candidate>().swap(cache[hidx].negative_candidates);

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