Fixed small memory leak in WFA2lib

waveygang · Jul 11, 2022 · 63a0da0 · 63a0da0
1 parent 164c1d5
commit 63a0da0
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Showing 3 changed files with 18 additions and 10 deletions.
diff --git a/src/common/wflign/deps/WFA/wavefront/wavefront_aligner.c b/src/common/wflign/deps/WFA/wavefront/wavefront_aligner.c
@@ -167,6 +167,9 @@ void wavefront_aligner_init_alignment(
     // Allocate subsidiary aligners
     wf_aligner->aligner_forward = wavefront_aligner_new(&subsidiary_attr);
     wf_aligner->aligner_reverse = wavefront_aligner_new(&subsidiary_attr);
+    // Allocate global CIGAR
+    cigar_allocate(&wf_aligner->bialign_cigar,
+        2*(pattern_length+text_length),wf_aligner->mm_allocator);
   } else {
     wf_aligner->aligner_forward = NULL;
     wf_aligner->aligner_reverse = NULL;
@@ -295,12 +298,15 @@ void wavefront_aligner_reap(
   // Padded sequences
   if (wf_aligner->sequences != NULL) {
     strings_padded_delete(wf_aligner->sequences);
+    wf_aligner->sequences = NULL;
   }
   // Wavefront components
   wavefront_components_reap(&wf_aligner->wf_components);
   // Subsidiary aligners
-  if (wf_aligner->aligner_forward != NULL) wavefront_aligner_reap(wf_aligner->aligner_forward);
-  if (wf_aligner->aligner_reverse != NULL) wavefront_aligner_reap(wf_aligner->aligner_reverse);
+  if (wf_aligner->bidirectional_alignment) {
+    wavefront_aligner_reap(wf_aligner->aligner_forward);
+    wavefront_aligner_reap(wf_aligner->aligner_reverse);
+  }
   // Slab
   wavefront_slab_reap(wf_aligner->wavefront_slab);
 }
@@ -316,8 +322,11 @@ void wavefront_aligner_delete(
   // Wavefront components
   wavefront_components_free(&wf_aligner->wf_components);
   // Subsidiary aligners
-  if (wf_aligner->aligner_forward != NULL) wavefront_aligner_delete(wf_aligner->aligner_forward);
-  if (wf_aligner->aligner_reverse != NULL) wavefront_aligner_delete(wf_aligner->aligner_reverse);
+  if (wf_aligner->bidirectional_alignment) {
+    wavefront_aligner_delete(wf_aligner->aligner_forward);
+    wavefront_aligner_delete(wf_aligner->aligner_reverse);
+    cigar_free(&wf_aligner->bialign_cigar);
+  }
   // CIGAR
   if (!score_only) {
     cigar_free(&wf_aligner->cigar);

diff --git a/src/common/wflign/deps/WFA/wavefront/wavefront_aligner.h b/src/common/wflign/deps/WFA/wavefront/wavefront_aligner.h
@@ -110,6 +110,7 @@ typedef struct _wavefront_aligner_t {
   wavefront_aligner_t* aligner_forward;       // Forward aligner
   wavefront_aligner_t* aligner_reverse;       // Reverse aligner
   wf_bialign_breakpoint_t bialign_breakpoint; // Breakpoint of two wavefronts (bialigner)
+  cigar_t bialign_cigar;                      // Global BiWFA Alignment CIGAR
   // CIGAR
   cigar_t cigar;                              // Alignment CIGAR
   // MM

diff --git a/src/common/wflign/deps/WFA/wavefront/wavefront_bialign.c b/src/common/wflign/deps/WFA/wavefront/wavefront_bialign.c
@@ -617,17 +617,15 @@ void wavefront_bialign(
   if (wf_aligner->alignment_scope == compute_score) {
     wavefront_bialign_compute_score(wf_aligner,pattern,pattern_length,text,text_length);
   } else {
-    cigar_t cigar;
-    cigar_allocate(&cigar,2*(pattern_length+text_length),wf_aligner->mm_allocator);
+    SWAP(wf_aligner->cigar,wf_aligner->bialign_cigar);
+    cigar_resize(&wf_aligner->bialign_cigar,2*(pattern_length+text_length));
     // Bidirectional alignment
     wavefront_bialign_alignment(wf_aligner,
         pattern,pattern_length,text,text_length,
         &wf_aligner->alignment_form,
         affine_matrix_M,affine_matrix_M,
-        INT_MAX,&cigar,0);
-    // Swap and free cigar
-    SWAP(wf_aligner->cigar,cigar);
-    cigar_free(&cigar);
+        INT_MAX,&wf_aligner->bialign_cigar,0);
+    SWAP(wf_aligner->cigar,wf_aligner->bialign_cigar);
   }
 }