Improve code readability. (bfb95030) · Commits · github_fork / Chromap

src/chromap.cc

+2 −2

Original line number	Diff line number	Diff line
		@@ -341,7 +341,7 @@ void Chromap::ComputeBarcodeAbundance(uint64_t max_num_sample_barcodes) {
		for (uint32_t barcode_index = 0; barcode_index < num_loaded_barcodes;
		++barcode_index) {
		std::vector<int> N_pos ; // position of Ns
		barcode_batch.GetSequenceNsAt(barcode_index, true, N_pos);
		barcode_batch.GetSequenceNsAt(barcode_index, /little_endian=/true, N_pos);
		if (N_pos.size() > 0) continue;

		uint32_t barcode_length =
		@@ -419,7 +419,7 @@ bool Chromap::CorrectBarcodeAt(uint32_t barcode_index,
		kh_get(k64_seq, barcode_whitelist_lookup_table_, barcode_key);
		std::vector<int> N_pos ; // position of Ns

		barcode_batch.GetSequenceNsAt(barcode_index, true, N_pos);
		barcode_batch.GetSequenceNsAt(barcode_index, /little_endian=/true, N_pos);
		if (N_pos.size() > (uint32_t)mapping_parameters_.barcode_correction_error_threshold) return false;

		if (N_pos.size() == 0 && barcode_whitelist_lookup_table_iterator !=

src/sequence_batch.cc

+6 −6

Original line number	Diff line number	Diff line
		@@ -30,12 +30,12 @@ uint32_t SequenceBatch::LoadBatch() {
		if (length > 0) {
		kseq_t *sequence = sequence_batch_[sequence_index];
		std::swap(sequence_kseq_->seq, sequence->seq);
		ReplaceByEffectiveRange(sequence->seq, true);
		ReplaceByEffectiveRange(sequence->seq, /is_seq=/true);
		std::swap(sequence_kseq_->name, sequence->name);
		std::swap(sequence_kseq_->comment, sequence->comment);
		if (sequence_kseq_->qual.l != 0) { // fastq file
		std::swap(sequence_kseq_->qual, sequence->qual);
		ReplaceByEffectiveRange(sequence->qual, false);
		ReplaceByEffectiveRange(sequence->qual, /is_seq=/false);
		}
		sequence->id = num_loaded_sequences_;
		++num_loaded_sequences_;
		@@ -71,14 +71,14 @@ bool SequenceBatch::LoadOneSequenceAndSaveAt(uint32_t sequence_index) {
		if (length > 0) {
		kseq_t *sequence = sequence_batch_[sequence_index];
		std::swap(sequence_kseq_->seq, sequence->seq);
		ReplaceByEffectiveRange(sequence->seq, true);
		ReplaceByEffectiveRange(sequence->seq, /is_seq=/true);
		std::swap(sequence_kseq_->name, sequence->name);
		std::swap(sequence_kseq_->comment, sequence->comment);
		sequence->id = num_loaded_sequences_;
		++num_loaded_sequences_;
		if (sequence_kseq_->qual.l != 0) { // fastq file
		std::swap(sequence_kseq_->qual, sequence->qual);
		ReplaceByEffectiveRange(sequence->qual, false);
		ReplaceByEffectiveRange(sequence->qual, /is_seq=/false);
		}
		} else {
		if (length != -1) {
		@@ -104,12 +104,12 @@ uint32_t SequenceBatch::LoadAllSequences() {
		sequence_batch_.emplace_back((kseq_t *)calloc(1, sizeof(kseq_t)));
		kseq_t *sequence = sequence_batch_.back();
		std::swap(sequence_kseq_->seq, sequence->seq);
		ReplaceByEffectiveRange(sequence->seq, true);
		ReplaceByEffectiveRange(sequence->seq, /is_seq=/true);
		std::swap(sequence_kseq_->name, sequence->name);
		std::swap(sequence_kseq_->comment, sequence->comment);
		if (sequence_kseq_->qual.l != 0) { // fastq file
		std::swap(sequence_kseq_->qual, sequence->qual);
		ReplaceByEffectiveRange(sequence->qual, false);
		ReplaceByEffectiveRange(sequence->qual, /is_seq=/false);
		}
		sequence->id = num_loaded_sequences_;
		++num_loaded_sequences_;

src/sequence_batch.h

+6 −5

Original line number	Diff line number	Diff line
		@@ -84,17 +84,18 @@ class SequenceBatch {
		// big_endian: N_pos is in the order of sequence
		// little_endian: N_pos is in the order from the sequence right side to left,
		// this is the order of the GenerateSeed
		// e.g: If the sequence is "ACN", big endian returns N at 2,
		// little endian returns N at 0.
		inline void GetSequenceNsAt(uint32_t sequence_index, bool little_endian, std::vector<int> &N_pos) {
		int l = sequence_batch_[sequence_index]->seq.l;
		char *s = sequence_batch_[sequence_index]->seq.s;
		int i;
		const int l = sequence_batch_[sequence_index]->seq.l;
		const char *s = sequence_batch_[sequence_index]->seq.s;
		N_pos.clear();
		if (little_endian) {
		for (i = l - 1; i >= 0; --i) {
		for (int i = l - 1; i >= 0; --i) {
		if (s[i] == 'N') N_pos.push_back(l - 1 - i);
		}
		} else {
		for (i = 0; i < l; ++i) {
		for (int i = 0; i < l; ++i) {
		if (s[i] == 'N') N_pos.push_back(i);
		}
		}

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