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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;
|
