Call ksw_gen_simple_mat only once

ksahlin · Mar 17, 2023 · 88ffb17 · 88ffb17
1 parent b70bf3c
commit 88ffb17
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Showing 2 changed files with 10 additions and 8 deletions.
diff --git a/src/aligner.cpp b/src/aligner.cpp
@@ -219,6 +219,8 @@ unsigned char seq_nt4_table[256] = {
     4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
 };
 
+}  // namespace
+
 void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
 {
     int i, j;
@@ -233,8 +235,6 @@ void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
         mat[(m - 1) * m + j] = 0;
 }
 
-}  // namespace
-
 aln_info Aligner::ksw_extend(const std::string& query, const std::string& ref, bool right_align) const {
     int w = -1; // band width; -1 is inf
     int zdrop = -1; // -1 to disable
@@ -245,10 +245,6 @@ aln_info Aligner::ksw_extend(const std::string& query, const std::string& ref, b
     ksw_extz_t ez;
     memset(&ez, 0, sizeof(ksw_extz_t));
 
-    int8_t m = 5;
-    int8_t mat[25];
-    ksw_gen_simple_mat(5, mat, parameters.match, -parameters.mismatch);
-
     ez.max_q = ez.max_t = ez.mqe_t = ez.mte_q = -1;
     ez.max = 0; ez.mqe = ez.mte = KSW_NEG_INF;
     ez.n_cigar = 0;
@@ -262,7 +258,7 @@ aln_info Aligner::ksw_extend(const std::string& query, const std::string& ref, b
         tseq[i] = seq_nt4_table[(uint8_t)ref[i]];
 
     ksw_extz2_sse(
-        nullptr, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, m, mat, parameters.gap_open, parameters.gap_extend, w, zdrop, parameters.end_bonus, flag, &ez
+        nullptr, qlen, (uint8_t*)qseq, tlen, (uint8_t*)tseq, ksw_matrix_m, ksw_matrix, parameters.gap_open, parameters.gap_extend, w, zdrop, parameters.end_bonus, flag, &ez
     );
     free(qseq);
     free(tseq);

diff --git a/src/aligner.hpp b/src/aligner.hpp
@@ -29,12 +29,16 @@ struct aln_info {
     int ref_span() const { return ref_end - ref_start; }
 };
 
+void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b);
+
 struct Aligner {
 public:
     Aligner(alignment_params parameters)
         : parameters(parameters)
         , ssw_aligner(StripedSmithWaterman::Aligner(parameters.match, parameters.mismatch, parameters.gap_open, parameters.gap_extend))
-    { }
+    {
+        ksw_gen_simple_mat(ksw_matrix_m, ksw_matrix, parameters.match, -parameters.mismatch);
+    }
 
     aln_info align(const std::string &query, const std::string &ref) const;
 
@@ -63,6 +67,8 @@ struct Aligner {
     const StripedSmithWaterman::Aligner ssw_aligner;
     const StripedSmithWaterman::Filter filter;
     mutable unsigned m_align_calls{0};  // no. of calls to the align() method
+    const int8_t ksw_matrix_m{5};
+    int8_t ksw_matrix[25];
 };
 
 inline int hamming_distance(const std::string &s, const std::string &t) {