Reformat with clang-format

ksahlin · Apr 26, 2023 · 5b55d0a · 5b55d0a
1 parent 0786f38
commit 5b55d0a
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Showing 38 changed files with 2,037 additions and 1,835 deletions.
diff --git a/src/aligner.cpp b/src/aligner.cpp
@@ -4,19 +4,19 @@
  * This is for anything that returns an aln_info object, currently
  * Aligner::align and hamming_align.
  */
-#include <sstream>
-#include <tuple>
+#include "aligner.hpp"
 #include <algorithm>
 #include <cassert>
-#include "aligner.hpp"
+#include <sstream>
+#include <tuple>
 
-aln_info Aligner::align(const std::string &query, const std::string &ref) const {
+aln_info Aligner::align(const std::string& query, const std::string& ref) const {
     m_align_calls++;
     aln_info aln;
     int32_t maskLen = query.length() / 2;
     maskLen = std::max(maskLen, 15);
-    if (ref.length() > 2000){
-//        std::cerr << "ALIGNMENT TO REF LONGER THAN 2000bp - REPORT TO DEVELOPER. Happened for read: " <<  query << " ref len:" << ref.length() << std::endl;
+    if (ref.length() > 2000) {
+        //        std::cerr << "ALIGNMENT TO REF LONGER THAN 2000bp - REPORT TO DEVELOPER. Happened for read: " <<  query << " ref len:" << ref.length() << std::endl;
         aln.edit_distance = 100000;
         aln.ref_start = 0;
         aln.sw_score = -1000000;
@@ -110,12 +110,16 @@ aln_info Aligner::align(const std::string &query, const std::string &ref) const
  * of the query, once for each end.
  */
 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
+    const std::string& query,
+    const std::string& ref,
+    int match,
+    int mismatch,
+    int end_bonus
 ) {
     size_t n = query.length();
 
-    size_t start = 0; // start of the current segment
-    int score = end_bonus; // accumulated score so far in the current segment
+    size_t start = 0;       // start of the current segment
+    int score = end_bonus;  // accumulated score so far in the current segment
 
     size_t best_start = 0;
     size_t best_end = 0;
@@ -144,15 +148,15 @@ std::tuple<size_t, size_t, int> highest_scoring_segment(
     return std::make_tuple(best_start, best_end, best_score);
 }
 
-aln_info hamming_align(
-    const std::string &query, const std::string &ref, int match, int mismatch, int end_bonus
-) {
+aln_info
+hamming_align(const std::string& query, const std::string& ref, int match, int mismatch, int end_bonus) {
     aln_info aln;
     if (query.length() != ref.length()) {
         return aln;
     }
 
-    auto [segment_start, segment_end, score] = highest_scoring_segment(query, ref, match, mismatch, end_bonus);
+    auto [segment_start, segment_end, score] =
+        highest_scoring_segment(query, ref, match, mismatch, end_bonus);
 
     Cigar cigar;
     if (segment_start > 0) {

diff --git a/src/aligner.hpp b/src/aligner.hpp
@@ -3,9 +3,8 @@
 
 #include <string>
 #include <tuple>
-#include "ssw/ssw_cpp.h"
 #include "cigar.hpp"
-
+#include "ssw/ssw_cpp.h"
 
 struct alignment_params {
     // match is a score, the others are penalties (all are nonnegative)
@@ -29,28 +28,30 @@ struct aln_info {
 };
 
 struct Aligner {
-public:
+   public:
     Aligner(alignment_params parameters)
         : parameters(parameters)
-        , ssw_aligner(StripedSmithWaterman::Aligner(parameters.match, parameters.mismatch, parameters.gap_open, parameters.gap_extend))
-    { }
+        , 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;
+    aln_info align(const std::string& query, const std::string& ref) const;
 
     alignment_params parameters;
 
-    unsigned calls_count() {
-        return m_align_calls;
-    }
+    unsigned calls_count() { return m_align_calls; }
 
-private:
+   private:
     const StripedSmithWaterman::Aligner ssw_aligner;
     const StripedSmithWaterman::Filter filter;
     mutable unsigned m_align_calls{0};  // no. of calls to the align() method
 };
 
-inline int hamming_distance(const std::string &s, const std::string &t) {
-    if (s.length() != t.length()){
+inline int hamming_distance(const std::string& s, const std::string& t) {
+    if (s.length() != t.length()) {
         return -1;
     }
 
@@ -65,11 +66,14 @@ inline int hamming_distance(const std::string &s, const std::string &t) {
 }
 
 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
+    const std::string& query,
+    const std::string& ref,
+    int match,
+    int mismatch,
+    int end_bonus
 );
 
-aln_info hamming_align(
-    const std::string &query, const std::string &ref, int match, int mismatch, int end_bonus
-);
+aln_info
+hamming_align(const std::string& query, const std::string& ref, int match, int mismatch, int end_bonus);
 
 #endif