Prodigal V2.60 bugfix 1

hyattpd · Jul 11, 2013 · 4bc33bd · 4bc33bd
1 parent 5770df5
commit 4bc33bd
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/dprog.c b/dprog.c
@@ -123,7 +123,7 @@ int dprog(struct _node *nod, int nn, struct _training *tinf, int flag) {
 void score_connection(struct _node *nod, int p1, int p2, struct _training *tinf,
                       int flag) {
   struct _node *n1 = &(nod[p1]), *n2 = &(nod[p2]), *n3;
-  int i, cod = 0, left = n1->ndx, right = n2->ndx, bnd, ovlp = 0, maxfr = -1;
+  int i, left = n1->ndx, right = n2->ndx, bnd, ovlp = 0, maxfr = -1;
   double score = 0.0, scr_mod = 0.0, maxval;
 
   /***********************/
@@ -158,7 +158,7 @@ void score_connection(struct _node *nod, int p1, int p2, struct _training *tinf,
           n2->type == STOP) {
     if(n2->stop_val >= n1->ndx) return;
     if(n1->ndx % 3 != n2->ndx % 3) return;
-    cod = 1; right += 2;
+    right += 2;
     if(flag == 0) scr_mod = tinf->bias[0]*n1->gc_score[0] +
                   tinf->bias[1]*n1->gc_score[1] + tinf->bias[2]*n1->gc_score[2];
     else if(flag == 1) score = n1->cscore + n1->sscore;
@@ -169,7 +169,7 @@ void score_connection(struct _node *nod, int p1, int p2, struct _training *tinf,
           n2->type != STOP) {
     if(n1->stop_val <= n2->ndx) return;
     if(n1->ndx % 3 != n2->ndx % 3) return;
-    cod = 1; left -= 2;
+    left -= 2;
     if(flag == 0) scr_mod = tinf->bias[0]*n2->gc_score[0] +
                   tinf->bias[1]*n2->gc_score[1] + tinf->bias[2]*n2->gc_score[2];
     else if(flag == 1) score = n2->cscore + n2->sscore;
@@ -246,7 +246,7 @@ void score_connection(struct _node *nod, int p1, int p2, struct _training *tinf,
     if(n2->stop_val >= n1->ndx) return;
     if(n1->star_ptr[n2->ndx%3] == -1) return;
     n3 = &(nod[n1->star_ptr[n2->ndx%3]]);
-    left = n3->ndx; right += 2; cod = 1;
+    left = n3->ndx; right += 2;
     if(flag == 0) scr_mod = tinf->bias[0]*n3->gc_score[0] +
                   tinf->bias[1]*n3->gc_score[1] + tinf->bias[2]*n3->gc_score[2];
     else if(flag == 1) score = n3->cscore + n3->sscore +
@@ -259,7 +259,7 @@ void score_connection(struct _node *nod, int p1, int p2, struct _training *tinf,
     if(n1->stop_val <= n2->ndx) return;
     if(n2->star_ptr[n1->ndx%3] == -1) return;
     n3 = &(nod[n2->star_ptr[n1->ndx%3]]);
-    left -= 2; right = n3->ndx; cod = 1;
+    left -= 2; right = n3->ndx;
     if(flag == 0) scr_mod = tinf->bias[0]*n3->gc_score[0] +
                   tinf->bias[1]*n3->gc_score[1] + tinf->bias[2]*n3->gc_score[2];
     else if(flag == 1) score = n3->cscore + n3->sscore +

diff --git a/gene.c b/gene.c
@@ -23,10 +23,10 @@
 /* Copies genes from the dynamic programming to a final array */
 
 int add_genes(struct _gene *glist, struct _node *nod, int dbeg) {
-  int path, pos, ctr;
+  int path, ctr;
 
   if(dbeg == -1) return 0;
-  path = dbeg; ctr = 0; pos = -1;  
+  path = dbeg; ctr = 0;
   while(nod[path].traceb != -1) path = nod[path].traceb;
 
   while(path != -1) {

diff --git a/sequence.c b/sequence.c
@@ -660,12 +660,12 @@ int shine_dalgarno_exact(unsigned char *seq, int pos, int start, double *rwt) {
   int i, j, k, mism, rdis, limit, max_val, cur_val = 0;
   double match[6], cur_ctr, dis_flag;
 
-  if(pos < 0) return 0;
   limit = imin(6, start-4-pos);
   for(i = limit; i < 6; i++) match[i] = -10.0;
 
   /* Compare the 6-base region to AGGAGG */
   for(i = 0; i < limit; i++) {
+    if(pos+i < 0) continue;
     if(i%3 == 0 && is_a(seq, pos+i) == 1) match[i] = 2.0;
     else if(i%3 != 0 && is_g(seq, pos+i) == 1) match[i] = 3.0;
     else match[i] = -10.0;
@@ -736,12 +736,12 @@ int shine_dalgarno_mm(unsigned char *seq, int pos, int start, double *rwt) {
   int i, j, k, mism, rdis, limit, max_val, cur_val = 0;
   double match[6], cur_ctr, dis_flag;
 
-  if(pos < 0) return 0;
   limit = imin(6, start-4-pos);
   for(i = limit; i < 6; i++) match[i] = -10.0;
 
   /* Compare the 6-base region to AGGAGG */
   for(i = 0; i < limit; i++) {
+    if(pos+i < 0) continue;
     if(i % 3 == 0) {
       if(is_a(seq, pos+i) == 1) match[i] = 2.0;
       else match[i] = -3.0;