From: Santiago Vila <sanvila@debian.org>
Subject: Apply changes to generated files

--- a/src/dnaindex/compressed_protein_index.c
+++ b/src/dnaindex/compressed_protein_index.c
@@ -199,7 +199,7 @@
 {
   fatal("For compressed protein indexes, impossible to add numbers directly");
 
-  return NULL;
+  return FALSE;
 }
 
 # line 226 "compressed_protein_index.dy"
--- a/src/dnaindex/kmer_assembly_error.c
+++ b/src/dnaindex/kmer_assembly_error.c
@@ -7,9 +7,9 @@
 # line 14 "kmer_assembly_error.dy"
 boolean lift_indel_error_KmerAssembly(KmerAssemblyIndex * kai,KmerAssemblyPath * real,KmerAssemblyPath * error,long int * start_labels,int label_len,int error_position,int error_len)
 {
-  int i,j,k,true;
+  int i,j,k,true_int;
 
-  for(i=0,true=0;i<error->stack_len && true<real->stack_len;i++,true++) {
+  for(i=0,true_int=0;i<error->stack_len && true_int<real->stack_len;i++,true_int++) {
     if( i == error_position ) {
       if( error_len > 0 ) {
 	for(j=0;j<error_len;) {
@@ -19,7 +19,7 @@
       } else {
 	error_len = abs(error_len);
 	for(j=0;j<error_len;) {
-	  true++;
+	  true_int++;
 	  j++;
 	}
       }
@@ -33,10 +33,10 @@
 	remove_sequence_label_KmerAssemblyLink(error->stack[i],start_labels[k]+i);
       }
 
-      if( real->stack[true] == NULL ) {
+      if( real->stack[true_int] == NULL ) {
 	fprintf(stderr,"issue - true path is missing a link!");
       } else {
-	add_sequence_label_KmerAssemblyLink(real->stack[true],start_labels[k]+i);
+	add_sequence_label_KmerAssemblyLink(real->stack[true_int],start_labels[k]+i);
       }
       if( error->stack[i] != NULL && error->stack[i]->sequence_label_len == 0 ) {
 	detach_KmerAssemblyLink(kai,error->stack[i]);
@@ -416,7 +416,7 @@
 
 
     /* recursively call for each possible path: if any return
-       true, return TRUE */
+       true_int, return TRUE */
 
     /*    fprintf(stderr,"paths are branching, real with %d, error with %d\n",real->next->next_len,error->next->next_len);*/
 
@@ -545,7 +545,7 @@
 
 
     /* recursively call for each possible path: if any return
-       true, return TRUE */
+       true_int, return TRUE */
 
     /*    fprintf(stderr,"paths are branching, real with %d, error with %d\n",real->next->next_len,error->next->next_len);*/
 
--- a/src/dnaindex/kmer_assembly_untangler.c
+++ b/src/dnaindex/kmer_assembly_untangler.c
@@ -547,7 +547,14 @@
 
       if( have_link == 1 ) {
 /*	fprintf(stderr," ..reverse TAIL.. untangling...\n"); */
-	lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len);
+	lift_backward_tangled_tail(
+		kai,
+		newpath->stack[newpath->stack_len-1],
+		path,
+		(int*)transferred_label,
+		transferred_pos,
+		transferred_len
+	);
       }
 
       /* pop off the top of this path */
@@ -578,7 +585,7 @@
 }
 
 
-# line 599 "kmer_assembly_untangler.dy"
+# line 606 "kmer_assembly_untangler.dy"
 void lift_forward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyPath * tail,long int * start_label,int label_len)
 {
   int i;
@@ -640,7 +647,7 @@
 
 
 
-# line 660 "kmer_assembly_untangler.dy"
+# line 667 "kmer_assembly_untangler.dy"
 void lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len)
 {
   int i;
@@ -698,7 +705,7 @@
   /* finished lift */
 }
 
-# line 717 "kmer_assembly_untangler.dy"
+# line 724 "kmer_assembly_untangler.dy"
 KmerAssemblyPath * lift_forward_tangled_KmerAssemblyPath(KmerAssemblyIndex * kai,KmerAssemblyPath * kap,long int * start_label,int label_len)
 {
   int i,j;
@@ -779,7 +786,7 @@
 
 
 
-# line 781 "kmer_assembly_untangler.c"
+# line 788 "kmer_assembly_untangler.c"
 /* Function:  hard_link_KmerAssemblyPath(obj)
  *
  * Descrip:    Bumps up the reference count of the object
--- a/src/models/est_evidence.c
+++ b/src/models/est_evidence.c
@@ -115,7 +115,7 @@
   in->utr_pot = est_utr_pot;
   in->cds_intron_pot = est_intron_pot;
   in->utr_intron_pot = est_intron_pot;
-  in->geu_free = free_EstEvidence;
+  in->geu_free = (int(*)(void*))free_EstEvidence;
   in->frameshift_cds = est_cds_frameshift;
   in->stop_pot = est_stop_pot;
   in->start_pot = est_start_pot;
--- a/src/models/genewisehsp.c
+++ b/src/models/genewisehsp.c
@@ -262,30 +262,30 @@
 
 
 # line 291 "genewisehsp.dy"
-int consistent_GeneWiseHSP(GeneWiseHSP * true,GeneWiseHSP * proposed)
+int consistent_GeneWiseHSP(GeneWiseHSP * true_val,GeneWiseHSP * proposed)
 {
   int query_centre;
   int target_centre;
 
-  assert(true);
+  assert(true_val);
   assert(proposed);
   /* is this left or right of the true HSP */
   query_centre = (proposed->query_start + proposed->query_end) / 2;
   target_centre = (proposed->target_start + proposed->target_end) / 2;
   
   /* overlap criteria first */
-  if( query_centre >= true->query_start && query_centre <= true->query_end ) {
+  if( query_centre >= true_val->query_start && query_centre <= true_val->query_end ) {
     return 0;
   }
   
   /* left or right */
-  if( query_centre > true->query_end ) {
-    if( target_centre < true->target_end ) {
+  if( query_centre > true_val->query_end ) {
+    if( target_centre < true_val->target_end ) {
       /* no - inconsistent */
       return 0;
     }
   } else {
-    if( target_centre > true->target_start ) {
+    if( target_centre > true_val->target_start ) {
       return 0;
     }
   }
@@ -293,7 +293,7 @@
 
   /* overlap */
 
-  if( target_centre >= true->target_start && target_centre <= true->target_end ) {
+  if( target_centre >= true_val->target_start && target_centre <= true_val->target_end ) {
     return 0;
   }
 
--- a/src/socket/functionclient.c
+++ b/src/socket/functionclient.c
@@ -181,7 +181,7 @@
   bcopy( hp->h_addr, &server.sin_addr, hp->h_length);
   server.sin_port = htons(port);
 
-  connect(out->socket, &server, sizeof(server));
+  connect(out->socket, (const struct sockaddr *)&server, sizeof(server));
   
 
   return out;