Fixed bug on internal-score conversion and refactor error-codes

wavefront/wavefront_align.c

@@ -252,15 +252,13 @@ void wavefront_align_terminate(
     wavefront_aligner_t* const wf_aligner,
     const int score) {
   // Parameters
-  const distance_metric_t distance_metric = wf_aligner->penalties.distance_metric;
   const int pattern_length = wf_aligner->pattern_length;
   const int text_length = wf_aligner->text_length;
-  const int swg_match_score = -(wf_aligner->penalties.match);
   // Retrieve alignment
   if (wf_aligner->alignment_scope == compute_score) {
     cigar_clear(&wf_aligner->cigar);
-    wf_aligner->cigar.score = (distance_metric <= edit) ? score :
-        WF_PENALTIES_GET_SW_SCORE(swg_match_score,pattern_length,text_length,score);
+    wf_aligner->cigar.score =
+        wavefront_get_classic_score(wf_aligner,pattern_length,text_length,score);
   } else {
     // Parameters
     wavefront_components_t* const wf_components = &wf_aligner->wf_components;
@@ -289,8 +287,8 @@ void wavefront_align_terminate(
       }
     }
     // Set score & finish
-    wf_aligner->cigar.score = (distance_metric <= edit) ? score :
-        WF_PENALTIES_GET_SW_SCORE(swg_match_score,pattern_length,text_length,score);
+    wf_aligner->cigar.score =
+        wavefront_get_classic_score(wf_aligner,pattern_length,text_length,score);
   }
   // Set successful
   wf_aligner->align_status.status = WF_STATUS_SUCCESSFUL;

wavefront/wavefront_aligner.c

@@ -49,19 +49,22 @@ char* wf_error_msg[] =
   /* WF_STATUS_OOM                  == -3 */ "[WFA] Alignment failed. Maximum memory threshold reached",
   /* WF_STATUS_MAX_SCORE_REACHED    == -2 */ "[WFA] Alignment failed. Maximum score reached",
   /* WF_STATUS_UNFEASIBLE           == -1 */ "[WFA] Alignment unfeasible (possible due to heuristic parameters)",
-  /* WF_STATUS_SUCCESSFUL           ==  0 */ "[WFA] Alignment successful",
-  /* WF_STATUS_IN_PROGRESS          ==  1 */ "[WFA] Alignment in progress",
+  /* WF_STATUS_SUCCESSFUL           ==  0 */ "[WFA] Alignment finished successfully",
 };
-char* wavefront_align_strerror(const int wf_error_code) {
-  return wf_error_msg[wf_error_code+3];
+char* wavefront_align_strerror(const int error_code) {
+  if (error_code > 0) {
+    fprintf(stderr,"[WFA] Internal alignment error code (%d)",error_code);
+    exit(1);
+  }
+  return wf_error_msg[error_code+3];
 }
 /*
  * Alignment status
  */
 void wavefront_align_status_clear(
-    wavefront_align_status_t* const wf_align_status) {
-  wf_align_status->status = WF_STATUS_IN_PROGRESS;
-  wf_align_status->score = 0;
+    wavefront_align_status_t* const align_status) {
+  align_status->status = WF_STATUS_SUCCESSFUL;
+  align_status->score = 0;
 }
 /*
  * Setup
@@ -344,6 +347,22 @@ void wavefront_aligner_delete(
     mm_allocator_delete(mm_allocator);
   }
 }
+/*
+ * Accessors
+ */
+int wavefront_get_classic_score(
+    wavefront_aligner_t* const wf_aligner,
+    const int pattern_length,
+    const int text_length,
+    const int wf_score) {
+  // Parameters
+  const int plen = wf_aligner->pattern_length;
+  const int tlen = wf_aligner->text_length;
+  const int swg_match = -(wf_aligner->penalties.match);
+  const distance_metric_t distance_metric = wf_aligner->penalties.distance_metric;
+  // Adapt score
+  return (distance_metric <= edit) ? wf_score : WF_SCORE_TO_SW_SCORE(swg_match,plen,tlen,wf_score);
+}
 /*
  * Span configuration
  */

wavefront/wavefront_aligner.h

@@ -50,14 +50,17 @@
 /*
  * Error codes & messages
  */
+// Success
 #define WF_STATUS_SUCCESSFUL               0
-#define WF_STATUS_IN_PROGRESS              1
-#define WF_STATUS_END_REACHED              2 /* Internal */
+// Errors
 #define WF_STATUS_UNFEASIBLE              -1
 #define WF_STATUS_MAX_SCORE_REACHED       -2
 #define WF_STATUS_OOM                     -3
+// Internal
+#define WF_STATUS_END_REACHED              1
+// Error messages
 extern char* wf_error_msg[5];
-char* wavefront_align_strerror(const int wf_error_code);
+char* wavefront_align_strerror(const int error_code);
 
 /*
  * Alignment status
@@ -142,6 +145,15 @@ void wavefront_aligner_reap(
 void wavefront_aligner_delete(
     wavefront_aligner_t* const wf_aligner);
 
+/*
+ * Accessors
+ */
+int wavefront_get_classic_score(
+    wavefront_aligner_t* const wf_aligner,
+    const int pattern_length,
+    const int text_length,
+    const int wf_score);
+
 /*
  * Span configuration
  */

wavefront/wavefront_bialign.c

@@ -605,10 +605,7 @@ void wavefront_bialign_alignment(
       breakpoint.score_reverse,cigar,rlevel+1);
   if (wf_aligner->align_status.status != WF_STATUS_SUCCESSFUL) return;
   // Set score
-  const distance_metric_t distance_metric = wf_aligner->penalties.distance_metric;
-  const int swg_match_score = wf_aligner->penalties.match;
-  cigar->score = (distance_metric <= edit) ? breakpoint.score :
-      WF_PENALTIES_GET_SW_SCORE(swg_match_score,pattern_length,text_length,breakpoint.score);
+  cigar->score = wavefront_get_classic_score(wf_aligner,pattern_length,text_length,breakpoint.score);
 }
 /*
  * Bidirectional compute score
@@ -638,11 +635,8 @@ void wavefront_bialign_compute_score(
     }
   }
   // Report score
-  const distance_metric_t distance_metric = wf_aligner->penalties.distance_metric;
-  const int swg_match_score = wf_aligner->penalties.match;
   cigar_clear(&wf_aligner->cigar);
-  wf_aligner->cigar.score = (distance_metric <= edit) ? breakpoint.score :
-      WF_PENALTIES_GET_SW_SCORE(swg_match_score,pattern_length,text_length,breakpoint.score);
+  wf_aligner->cigar.score = wavefront_get_classic_score(wf_aligner,pattern_length,text_length,breakpoint.score);
   wf_aligner->align_status.status = WF_STATUS_SUCCESSFUL;
 }
 /*

wavefront/wavefront_debug.c

@@ -132,7 +132,7 @@ void wavefront_report_lite(
   // Banner
   fprintf(stream,"[WFA::Debug]");
   // Sequences
-  fprintf(stream,"\t%d",-wf_aligner->cigar.score);
+  fprintf(stream,"\t%d",wf_aligner->cigar.score);
   fprintf(stream,"\t%d\t%d",pattern_length,text_length);
   fprintf(stream,"\t%s",(status==0) ? "OK" : "FAIL");
   fprintf(stream,"\t%2.3f",TIMER_GET_TOTAL_MS(&wf_aligner->system.timer));
@@ -207,7 +207,7 @@ void wavefront_report_verbose_end(
   fprintf(stream,"\n");
   fprintf(stream,"[WFA::Debug]\tMemory.used\t%luMB\n",
       CONVERT_B_TO_MB(wf_aligner->align_status.memory_used));
-  fprintf(stream,"[WFA::Debug]\tWFA.score\t%d\n",-(wf_aligner->cigar.score));
+  fprintf(stream,"[WFA::Debug]\tWFA.score\t%d\n",wf_aligner->cigar.score);
   fprintf(stream,"[WFA::Debug]\tWFA.cigar\t");
   cigar_print(stream,&wf_aligner->cigar,true);
   fprintf(stream,"\n");

wavefront/wavefront_penalties.h

@@ -63,8 +63,7 @@ typedef struct {
 /*
  * Compute SW-score equivalent (thanks to Eizenga's formula)
  */
-#define WF_PENALTIES_GET_SW_SCORE(swg_match_score,plen,tlen,wf_score) \
-  (swg_match_score*(plen+tlen))/2 - wf_score
+#define WF_SCORE_TO_SW_SCORE(swg_match,plen,tlen,wf_score) ((swg_match*(plen+tlen) - wf_score)/2)
 
 /*
  * Penalties adjustment