Do not do the reverse-complement operation on the quality score when reversing. (59e405c3) · Commits · github_fork / Chromap

src/sequence_batch.cc

+11 −9

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);
		ReplaceByEffectiveRange(sequence->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);
		ReplaceByEffectiveRange(sequence->qual, 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);
		ReplaceByEffectiveRange(sequence->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);
		ReplaceByEffectiveRange(sequence->qual, 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);
		ReplaceByEffectiveRange(sequence->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);
		ReplaceByEffectiveRange(sequence->qual, false);
		}
		sequence->id = num_loaded_sequences_;
		++num_loaded_sequences_;
		@@ -137,7 +137,7 @@ void SequenceBatch::FinalizeLoading() {
		gzclose(sequence_file_);
		}

		void SequenceBatch::ReplaceByEffectiveRange(kstring_t &seq) {
		void SequenceBatch::ReplaceByEffectiveRange(kstring_t &seq, bool is_seq) {
		if (effective_range_[0] == 0 && effective_range_[1] == -1 &&
		effective_range_[2] == 1) {
		return;
		@@ -152,9 +152,11 @@ void SequenceBatch::ReplaceByEffectiveRange(kstring_t &seq) {
		seq.s[i] = '\0';
		seq.l = end - start + 1;
		if (effective_range_[2] == -1) {
		if (is_seq) {
		for (i = 0; i < (int)seq.l; ++i) {
		seq.s[i] = Uint8ToChar(((uint8_t)3) ^ (CharToUint8(seq.s[i])));
		}
		}
		for (i = 0, j = seq.l - 1; i < j; ++i, --j) {
		char tmp = seq.s[i];
		seq.s[i] = seq.s[j];

src/sequence_batch.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -211,7 +211,7 @@ class SequenceBatch {
		}

		protected:
		void ReplaceByEffectiveRange(kstring_t &seq);
		void ReplaceByEffectiveRange(kstring_t &seq, bool is_seq);

		uint32_t num_loaded_sequences_ = 0;
		uint32_t max_num_sequences_ = 0;

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