scan up to 50k hit and prioritize the hits by (overlap length - overh…

…ang length)

LA4Falcon.c

@@ -68,6 +68,7 @@
 
 typedef struct {
     int r_id;
+    int score;
     int t_o;
     int t_s;
     int t_e;
@@ -76,12 +77,10 @@ typedef struct {
 
 hit_record * hits;
 
+#define MIN(X,Y)  ((X) < (Y)) ? (X) : (Y) 
+
 static int compare_hits(const void  * h1, const void *h2) {
-    int ovl_len1;
-    int ovl_len2;
-    ovl_len1 = ((hit_record *) h1)->t_e - ((hit_record *) h1)->t_s;
-    ovl_len2 = ((hit_record *) h2)->t_e - ((hit_record *) h2)->t_s;
-    return ovl_len2 - ovl_len1;
+    return ((hit_record *) h2)->score - ((hit_record *) h1)->score;
 }
 
 
@@ -414,7 +413,7 @@ int main(int argc, char *argv[])
         abuffer = New_Read_Buffer(db1);
         bbuffer = New_Read_Buffer(db2);
         if (FALCON) {
-            hits = calloc(sizeof(hit_record), 4096);
+            hits = calloc(sizeof(hit_record), 50001);
             hit_count = 0;
         }
       }
@@ -639,13 +638,19 @@ int main(int argc, char *argv[])
             }
 
             if (skip_rest == 0) {
+                int ovl_len, overhang_len, score;
+                ovl_len = ovl->path.bepos - ovl->path.bbpos;
+                overhang_len = MIN( ovl->path.abpos, ovl->path.bbpos );
+                overhang_len +=  MIN(  aln->alen - ovl->path.aepos,  aln->blen - ovl->path.bepos);
+                score = ovl_len - overhang_len;
                 hits[hit_count].r_id = ovl->bread;
                 hits[hit_count].t_o = COMP(aln->flags);
                 hits[hit_count].t_s = ovl->path.bbpos;
                 hits[hit_count].t_e = ovl->path.bepos;
                 hits[hit_count].t_l = aln->blen;
+                hits[hit_count].score = score; 
                 hit_count ++;
-                if (hit_count > MAX_HIT_COUNT * 2) skip_rest = 1;
+                if (hit_count > 50000) skip_rest = 1;
 
 #undef TEST_ALN_OUT
 #ifdef TEST_ALN_OUT