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More refactorings #337

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merged 11 commits into from
Sep 6, 2023
Merged

More refactorings #337

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57a616a
Remove unused align_segment function
marcelm Sep 6, 2023
95eb719
Rename get_alignment to extend_seed
marcelm Sep 6, 2023
217ad79
Rename aln_info to AlignmentInfo
marcelm Sep 6, 2023
304e74a
Rename alignment_params to AlignmentParameters
marcelm Sep 6, 2023
7730f63
Rename i_dist_est to InsertSizeDistribution
marcelm Sep 6, 2023
04d3798
Replace score comparison function with a single templatized one
marcelm Sep 6, 2023
fac7932
Update comments
marcelm Sep 6, 2023
6b5e096
Simplify rescue_mate
marcelm Sep 6, 2023
7b38f95
Remove an unnecessary call to reverse_nam_if_needed()
marcelm Sep 6, 2023
8a839dd
Simplify
marcelm Sep 6, 2023
337c1de
Let rescue_mate return an Alignment
marcelm Sep 6, 2023
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8 changes: 4 additions & 4 deletions src/aligner.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,9 @@
#include <cassert>
#include "aligner.hpp"

aln_info Aligner::align(const std::string &query, const std::string &ref) const {
AlignmentInfo Aligner::align(const std::string &query, const std::string &ref) const {
m_align_calls++;
aln_info aln;
AlignmentInfo aln;
int32_t maskLen = query.length() / 2;
maskLen = std::max(maskLen, 15);
if (ref.length() > 2000){
Expand Down Expand Up @@ -150,10 +150,10 @@ std::tuple<size_t, size_t, int> highest_scoring_segment(
return std::make_tuple(best_start, best_end, best_score);
}

aln_info hamming_align(
AlignmentInfo hamming_align(
const std::string &query, const std::string &ref, int match, int mismatch, int end_bonus
) {
aln_info aln;
AlignmentInfo aln;
if (query.length() != ref.length()) {
return aln;
}
Expand Down
12 changes: 6 additions & 6 deletions src/aligner.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
#include "cigar.hpp"


struct alignment_params {
struct AlignmentParameters {
// match is a score, the others are penalties (all are nonnegative)
int match;
int mismatch;
Expand All @@ -16,7 +16,7 @@ struct alignment_params {
int end_bonus;
};

struct aln_info {
struct AlignmentInfo {
Cigar cigar;
unsigned int edit_distance{0};
unsigned int ref_start{0};
Expand All @@ -30,14 +30,14 @@ struct aln_info {

struct Aligner {
public:
Aligner(alignment_params parameters)
Aligner(AlignmentParameters parameters)
: parameters(parameters)
, ssw_aligner(StripedSmithWaterman::Aligner(parameters.match, parameters.mismatch, parameters.gap_open, parameters.gap_extend))
{ }

aln_info align(const std::string &query, const std::string &ref) const;
AlignmentInfo align(const std::string &query, const std::string &ref) const;

alignment_params parameters;
AlignmentParameters parameters;

unsigned calls_count() {
return m_align_calls;
Expand Down Expand Up @@ -68,7 +68,7 @@ std::tuple<size_t, size_t, int> highest_scoring_segment(
const std::string& query, const std::string& ref, int match, int mismatch, int end_bonus
);

aln_info hamming_align(
AlignmentInfo hamming_align(
const std::string &query, const std::string &ref, int match, int mismatch, int end_bonus
);

Expand Down
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