Separate header for Candidate. (7b69c877) · Commits · github_fork / Chromap

src/candidate.h

0 → 100644

+21 −0

Original line number	Diff line number	Diff line
		#ifndef CANDIDATE_H_
		#define CANDIDATE_H_

		namespace chromap {

		struct Candidate {
		uint64_t position;
		uint8_t count;

		bool operator<(const Candidate &c) const {
		if (count != c.count) {
		return count > c.count;
		}

		return position < c.position;
		}
		};

		} // namespace chromap

		#endif // CANDIDATE_H_

src/chromap.cc

+12 −12

Original line number	Diff line number	Diff line
		@@ -1321,14 +1321,14 @@ void Chromap<MappingRecord>::MapPairedEndReads() {

		read_batch1.SetSeqEffectiveRange(read1_format_[0], read1_format_[1], 1);
		read_batch2.SetSeqEffectiveRange(read2_format_[0], read2_format_[1], 1);
		barcode_batch.SetSeqEffectiveRange(barcode_format_[0], barcode_format_[1], barcode_format_[2]);
		barcode_batch.SetSeqEffectiveRange(barcode_format_[0], barcode_format_[1],
		barcode_format_[2]);
		read_batch1_for_loading.SetSeqEffectiveRange(read1_format_[0],
		read1_format_[1], 1);
		read_batch2_for_loading.SetSeqEffectiveRange(read2_format_[0],
		read2_format_[1], 1);
		barcode_batch_for_loading.SetSeqEffectiveRange(barcode_format_[0],
		barcode_format_[1],
		barcode_format_[2]);
		barcode_batch_for_loading.SetSeqEffectiveRange(
		barcode_format_[0], barcode_format_[1], barcode_format_[2]);

		// Initialize cache
		mm_cache mm_to_candidates_cache(2000003);
		@@ -2756,10 +2756,10 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		read_batch.SetSeqEffectiveRange(read1_format_[0], read1_format_[1], 1);
		read_batch_for_loading.SetSeqEffectiveRange(read1_format_[0],
		read1_format_[1], 1);
		barcode_batch.SetSeqEffectiveRange(barcode_format_[0], barcode_format_[1], barcode_format_[2]);
		barcode_batch_for_loading.SetSeqEffectiveRange(barcode_format_[0],
		barcode_format_[1],
		barcode_batch.SetSeqEffectiveRange(barcode_format_[0], barcode_format_[1],
		barcode_format_[2]);
		barcode_batch_for_loading.SetSeqEffectiveRange(
		barcode_format_[0], barcode_format_[1], barcode_format_[2]);

		mappings_on_diff_ref_seqs_.reserve(num_reference_sequences);
		deduped_mappings_on_diff_ref_seqs_.reserve(num_reference_sequences);

src/mapping_metadata.h

+2 −11

Original line number	Diff line number	Diff line
		@@ -5,18 +5,9 @@
		#include <utility>
		#include <vector>

		namespace chromap {
		#include "candidate.h"

		struct Candidate {
		uint64_t position;
		uint8_t count;
		bool operator<(const Candidate &c) const {
		if (count != c.count)
		return count > c.count;
		else
		return position < c.position;
		}
		};
		namespace chromap {

		class mm_cache;
		class Index;

src/sequence_batch.h

+5 −4

Original line number	Diff line number	Diff line
		@@ -212,7 +212,8 @@ class SequenceBatch {
		static constexpr char uint8_to_char_table_[8] = {'A', 'C', 'G', 'T',
		'N', 'N', 'N', 'N'};
		void ReplaceByEffectiveRange(kstring_t &seq) {
		if (effective_range_[0] == 0 && effective_range_[1] == -1 && effective_range_[2] == 1) {
		if (effective_range_[0] == 0 && effective_range_[1] == -1 &&
		effective_range_[2] == 1) {
		return;
		}
		int i, j;

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