fix: Use biWFA for smaller sequences or very high identity matches

waveygang · Oct 28, 2024 · 263321c · 263321c
1 parent 907a16e
commit 263321c
Showing 1 changed file with 19 additions and 40 deletions.
diff --git a/src/common/wflign/src/wflign.cpp b/src/common/wflign/src/wflign.cpp
@@ -53,22 +53,23 @@ void do_biwfa_alignment(
     const int status = wf_aligner.alignEnd2End(target, (int)target_length, query, (int)query_length);
 
     if (status == 0) { // WF_STATUS_SUCCESSFUL
-        // Create alignment record on heap
-        auto* aln = new alignment_t();
-        aln->ok = true;
-        aln->j = 0;
-        aln->i = 0;
-        aln->query_length = query_length;
-        aln->target_length = target_length;
+        // Create alignment record on stack
+        alignment_t aln;
+        aln.ok = true;
+        aln.j = 0;
+        aln.i = 0;
+        aln.query_length = query_length;
+        aln.target_length = target_length;
+        aln.is_rev = false;
 
         // Copy alignment CIGAR
-        wflign_edit_cigar_copy(wf_aligner, &aln->edit_cigar);
+        wflign_edit_cigar_copy(wf_aligner, &aln.edit_cigar);
 
         // Write alignment
         if (paf_format_else_sam) {
             write_alignment_paf(
                 out,
-                *aln,  // Dereference the pointer
+                aln,
                 query_name,
                 query_total_length,
                 query_offset,
@@ -81,48 +82,26 @@ void do_biwfa_alignment(
                 min_identity,
                 mashmap_estimated_identity);
         } else {
-            write_merged_alignment(
+            // Write SAM output directly
+            write_alignment_sam(
                 out,
-                {aln},  // Pass pointer to alignment
-                wf_aligner,
-                penalties,
-                emit_md_tag,
-                paf_format_else_sam,
-                no_seq_in_sam,
-                query,
+                aln,
                 query_name,
                 query_total_length,
                 query_offset,
                 query_length,
                 query_is_rev,
-                target,
                 target_name,
                 target_total_length,
                 target_offset,
                 target_length,
                 min_identity,
-#ifdef WFA_PNG_TSV_TIMING
-                0, // elapsed_time_wflambda_ms
-                1, // num_alignments 
-                1, // num_alignments_performed
-#endif
                 mashmap_estimated_identity,
-                wflign_max_len_minor,
-                wflign_max_len_minor,
-                0, // erode_k
-                0, // chain_gap
-                0, // max_patching_score
-                0, // min_inversion_length
-                MIN_WF_LENGTH,
-                0  // wf_max_dist_threshold
-#ifdef WFA_PNG_TSV_TIMING
-                ,
-                nullptr, // prefix_wavefront_plot_in_png
-                0,      // wfplot_max_size
-                false,  // emit_patching_tsv
-                nullptr // out_patching_tsv
-#endif
-                );
+                no_seq_in_sam,
+                emit_md_tag,
+                query,
+                target,
+                0); // No target pointer shift for biwfa
         }
     }
 }
@@ -467,7 +446,7 @@ void WFlign::wflign_affine_wavefront(
 
     // Use biWFA for smaller sequences or very high identity matches
 
-    if (!force_wflign) {
+    if (!force_wflign && (query_length <= MAX_LEN_FOR_STANDARD_WFA || target_length <= MAX_LEN_FOR_STANDARD_WFA)) {
         do_biwfa_alignment(
             query_name, query, query_total_length, query_offset, query_length, query_is_rev,
             target_name, target, target_total_length, target_offset, target_length,