Implemented heuristic additional methods

vgteam · Mar 7, 2022 · 684b6d4 · 684b6d4
1 parent bb9744a
commit 684b6d4
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Showing 27 changed files with 1,859 additions and 1,153 deletions.
diff --git a/README.md b/README.md
diff --git a/alignment/cigar.c b/alignment/cigar.c
@@ -105,7 +105,7 @@ void cigar_add_mismatches(
         ++p;
         break;
       default:
-        fprintf(stderr,"Aband-gaba. Wrong edit operation\n");
+        fprintf(stderr,"[CIGAR] Wrong edit operation\n");
         exit(1);
         break;
     }
@@ -171,7 +171,7 @@ int cigar_score_gap_affine(
         score -= penalties->gap_extension + ((last_op=='I') ? 0 : penalties->gap_opening);
         break;
       default:
-        fprintf(stderr,"Computing CIGAR score: Unknown operation\n");
+        fprintf(stderr,"[CIGAR] Computing CIGAR score: Unknown operation\n");
         exit(1);
     }
     last_op = cigar->operations[i];
@@ -194,7 +194,7 @@ int cigar_score_gap_affine2p_get_operations_score(
       return MIN(score1,score2);
     }
     default:
-      fprintf(stderr,"Computing CIGAR score: Unknown operation\n");
+      fprintf(stderr,"[CIGAR] Computing CIGAR score: Unknown operation\n");
       exit(1);
   }
 }
@@ -270,7 +270,7 @@ bool cigar_check_alignment(
         if (pattern[pattern_pos] != text[text_pos]) {
           if (verbose) {
             fprintf(stream,
-                "Align Check. Alignment not matching (pattern[%d]=%c != text[%d]=%c)\n",
+                "[AlignCheck] Alignment not matching (pattern[%d]=%c != text[%d]=%c)\n",
                 pattern_pos,pattern[pattern_pos],text_pos,text[text_pos]);
           }
           return false;
@@ -283,7 +283,7 @@ bool cigar_check_alignment(
         if (pattern[pattern_pos] == text[text_pos]) {
           if (verbose) {
             fprintf(stream,
-                "Align Check. Alignment not mismatching (pattern[%d]=%c == text[%d]=%c)\n",
+                "[AlignCheck] Alignment not mismatching (pattern[%d]=%c == text[%d]=%c)\n",
                 pattern_pos,pattern[pattern_pos],text_pos,text[text_pos]);
           }
           return false;
@@ -298,7 +298,7 @@ bool cigar_check_alignment(
         ++pattern_pos;
         break;
       default:
-        fprintf(stderr,"CIGAR check. Unknown edit operation '%c'\n",operations[i]);
+        fprintf(stderr,"[AlignCheck] Unknown edit operation '%c'\n",operations[i]);
         exit(1);
         break;
     }
@@ -307,15 +307,15 @@ bool cigar_check_alignment(
   if (pattern_pos != pattern_length) {
     if (verbose) {
       fprintf(stream,
-          "Align Check. Alignment incorrect length (pattern-aligned=%d,pattern-length=%d)\n",
+          "[AlignCheck] Alignment incorrect length (pattern-aligned=%d,pattern-length=%d)\n",
           pattern_pos,pattern_length);
     }
     return false;
   }
   if (text_pos != text_length) {
     if (verbose) {
       fprintf(stream,
-          "Align Check. Alignment incorrect length (text-aligned=%d,text-length=%d)\n",
+          "[AlignCheck] Alignment incorrect length (text-aligned=%d,text-length=%d)\n",
           text_pos,text_length);
     }
     return false;

diff --git a/bindings/cpp/WFAligner.cpp b/bindings/cpp/WFAligner.cpp
@@ -63,41 +63,34 @@ WFAligner::~WFAligner() {
 /*
  * Align End-to-end
  */
-int WFAligner::alignEnd2EndLambda(
+WFAligner::AlignmentStatus WFAligner::alignEnd2EndLambda(
     const int patternLength,
     const int textLength) {
   // Configure
   wavefront_aligner_set_alignment_end_to_end(wfAligner);
   // Align (using custom matching function)
-  return wavefront_align(wfAligner,
-      NULL,patternLength,
-      NULL,textLength);
+  return (WFAligner::AlignmentStatus) wavefront_align(wfAligner,NULL,patternLength,NULL,textLength);
 }
-int WFAligner::alignEnd2End(
+WFAligner::AlignmentStatus WFAligner::alignEnd2End(
     const char* const pattern,
     const int patternLength,
     const char* const text,
     const int textLength) {
   // Configure
   wavefront_aligner_set_alignment_end_to_end(wfAligner);
   // Align
-  return wavefront_align(wfAligner,
-      pattern,patternLength,
-      text,textLength);
+  return (WFAligner::AlignmentStatus) wavefront_align(wfAligner,pattern,patternLength,text,textLength);
 }
-int WFAligner::alignEnd2End(
+WFAligner::AlignmentStatus WFAligner::alignEnd2End(
     std::string& pattern,
     std::string& text) {
   // Delegate
-  return alignEnd2End(
-      pattern.c_str(),pattern.length(),
-      text.c_str(),text.length());
+  return alignEnd2End(pattern.c_str(),pattern.length(),text.c_str(),text.length());
 }
 /*
  * Align Ends-free
  */
-// Align Ends-free
-int WFAligner::alignEndsFreeLambda(
+WFAligner::AlignmentStatus WFAligner::alignEndsFreeLambda(
     const int patternLength,
     const int patternBeginFree,
     const int patternEndFree,
@@ -109,11 +102,9 @@ int WFAligner::alignEndsFreeLambda(
       patternBeginFree,patternEndFree,
       textBeginFree,textEndFree);
   // Align (using custom matching function)
-  return wavefront_align(wfAligner,
-      NULL,patternLength,
-      NULL,textLength);
+  return (WFAligner::AlignmentStatus) wavefront_align(wfAligner,NULL,patternLength,NULL,textLength);
 }
-int WFAligner::alignEndsFree(
+WFAligner::AlignmentStatus WFAligner::alignEndsFree(
     const char* const pattern,
     const int patternLength,
     const int patternBeginFree,
@@ -127,11 +118,9 @@ int WFAligner::alignEndsFree(
       patternBeginFree,patternEndFree,
       textBeginFree,textEndFree);
   // Align
-  return wavefront_align(wfAligner,
-      pattern,patternLength,
-      text,textLength);
+  return (WFAligner::AlignmentStatus) wavefront_align(wfAligner,pattern,patternLength,text,textLength);
 }
-int WFAligner::alignEndsFree(
+WFAligner::AlignmentStatus WFAligner::alignEndsFree(
     std::string& pattern,
     const int patternBeginFree,
     const int patternEndFree,
@@ -144,16 +133,50 @@ int WFAligner::alignEndsFree(
       text.c_str(),text.length());
 }
 /*
- * Reduction
+ * Alignment resume
+ */
+WFAligner::AlignmentStatus WFAligner::alignResume() {
+  // Resume alignment
+  return (WFAligner::AlignmentStatus) wavefront_align_resume(wfAligner);
+}
+/*
+ * Heuristics
  */
-void WFAligner::setReductionNone() {
-  wavefront_aligner_set_reduction_none(wfAligner);
+void WFAligner::setHeuristicNone() {
+  wavefront_aligner_set_heuristic_none(wfAligner);
+}
+void WFAligner::setHeuristicBandedStatic(
+    const int band_min_k,
+    const int band_max_k) {
+  wavefront_aligner_set_heuristic_banded_static(
+      wfAligner,band_min_k,band_max_k);
+}
+void WFAligner::setHeuristicBandedAdaptive(
+    const int band_min_k,
+    const int band_max_k,
+    const int steps_between_cutoffs) {
+  wavefront_aligner_set_heuristic_banded_adaptive(
+      wfAligner,band_min_k,band_max_k,steps_between_cutoffs);
 }
-void WFAligner::setReductionAdaptive(
+void WFAligner::setHeuristicWFadaptive(
     const int min_wavefront_length,
-    const int max_distance_threshold) {
-  wavefront_aligner_set_reduction_adaptive(
-      wfAligner,min_wavefront_length,max_distance_threshold);
+    const int max_distance_threshold,
+    const int steps_between_cutoffs) {
+  wavefront_aligner_set_heuristic_wfadaptive(
+      wfAligner,min_wavefront_length,
+      max_distance_threshold,steps_between_cutoffs);
+}
+void WFAligner::setHeuristicXDrop(
+    const int xdrop,
+    const int steps_between_cutoffs) {
+  wavefront_aligner_set_heuristic_xdrop(
+      wfAligner,xdrop,steps_between_cutoffs);
+}
+void WFAligner::setHeuristicZDrop(
+    const int zdrop,
+    const int steps_between_cutoffs) {
+  wavefront_aligner_set_heuristic_zdrop(
+      wfAligner,zdrop,steps_between_cutoffs);
 }
 /*
  * Custom extend-match function (lambda)

diff --git a/bindings/cpp/WFAligner.hpp b/bindings/cpp/WFAligner.hpp
@@ -59,27 +59,33 @@ class WFAligner {
     Score,
     Alignment,
   };
+  enum AlignmentStatus {
+    StatusSuccessful = WF_STATUS_SUCCESSFUL,
+    StatusDropped = WF_STATUS_HEURISTICALY_DROPPED,
+    StatusMaxScoreReached = WF_STATUS_MAX_SCORE_REACHED,
+    StatusOOM = WF_STATUS_OOM,
+  };
   // Align End-to-end
-  int alignEnd2EndLambda(
+  AlignmentStatus alignEnd2EndLambda(
       const int patternLength,
       const int textLength);
-  int alignEnd2End(
+  AlignmentStatus alignEnd2End(
       const char* const pattern,
       const int patternLength,
       const char* const text,
       const int textLength);
-  int alignEnd2End(
+  AlignmentStatus alignEnd2End(
       std::string& pattern,
       std::string& text);
   // Align Ends-free
-  int alignEndsFreeLambda(
+  AlignmentStatus alignEndsFreeLambda(
       const int patternLength,
       const int patternBeginFree,
       const int patternEndFree,
       const int textLength,
       const int textBeginFree,
       const int textEndFree);
-  int alignEndsFree(
+  AlignmentStatus alignEndsFree(
       const char* const pattern,
       const int patternLength,
       const int patternBeginFree,
@@ -88,18 +94,34 @@ class WFAligner {
       const int textLength,
       const int textBeginFree,
       const int textEndFree);
-  int alignEndsFree(
+  AlignmentStatus alignEndsFree(
       std::string& pattern,
       const int patternBeginFree,
       const int patternEndFree,
       std::string& text,
       const int textBeginFree,
       const int textEndFree);
-  // Reduction
-  void setReductionNone();
-  void setReductionAdaptive(
-      const int minWavefrontLength,
-      const int maxDistanceThreshold);
+  // Alignment resume
+  AlignmentStatus alignResume();
+  // Heuristics
+  void setHeuristicNone();
+  void setHeuristicBandedStatic(
+      const int band_min_k,
+      const int band_max_k);
+  void setHeuristicBandedAdaptive(
+      const int band_min_k,
+      const int band_max_k,
+      const int steps_between_cutoffs);
+  void setHeuristicWFadaptive(
+      const int min_wavefront_length,
+      const int max_distance_threshold,
+      const int steps_between_cutoffs);
+  void setHeuristicXDrop(
+      const int xdrop,
+      const int steps_between_cutoffs);
+  void setHeuristicZDrop(
+      const int zdrop,
+      const int steps_between_cutoffs);
   // Custom extend-match function (lambda)
   void setMatchFunct(
       int (*matchFunct)(int,int,void*),