ALignment: fixed a bug where a similarity threshold of 100% would

generate memory bugs

libfasta/fasta_header_handler.c

@@ -69,15 +69,34 @@ char* fastaSeqPtr_header_add_field(fastaSeqPtr seq, char* name, char* value)
 element_from_header* table_header_add_field(element_from_header* header, char* name, char* value)
 {
 	int nbf;
+	int i, j;
+	element_from_header* new_header;
+
 	nbf = atoi(header[0].value);
-	nbf++;
-	header = (element_from_header*) realloc(header, (nbf+1)*sizeof(element_from_header));
-	header[nbf].name = (char*) malloc((1+strlen(name))*sizeof(char));
-	strcpy(header[nbf].name, name);
-	header[nbf].value = (char*) malloc((1+strlen(value))*sizeof(char));
-	strcpy(header[nbf].value, value);
-	sprintf(header[0].value, "%d", nbf);
-	return(header);
+	new_header = (element_from_header*) realloc(header, ((nbf+1)*sizeof(element_from_header)));
+
+	i=0;
+	while ((strcmp(new_header[i].name, "definition") != 0) && (i < nbf))
+		i++;
+
+	if (strcmp(new_header[i].name, "definition") == 0)
+	{
+		j = nbf-1;
+		while (strcmp(new_header[j].name, "definition") == 0)
+		{
+			new_header[j+1].name = new_header[j].name;
+			new_header[j+1].value = new_header[j].value;
+			j--;
+		}
+	}
+
+	new_header[i].name = (char*) malloc((1+strlen(name))*sizeof(char));
+	strcpy(new_header[i].name, name);
+	new_header[i].value = (char*) malloc((1+strlen(value))*sizeof(char));
+	strcpy(new_header[i].value, value);
+	sprintf(new_header[0].value, "%d", nbf+1);
+
+	return(new_header);
 }
 
 
@@ -86,7 +105,7 @@ void free_header_table(element_from_header* header)
 	int i;
 	int nbf = atoi(header[0].value);
 
-	for (i = 0; i <= nbf; i++)
+	for (i = 0; i < nbf; i++)
 	{
 		free((header[i]).name);
 	    free((header[i]).value);
@@ -101,7 +120,7 @@ char* getItemFromHeader(char* name, element_from_header* header)
 	int nbf;
 	int i;
 	nbf = atoi(header[0].value);
-	for (i = 1; i <= nbf; i++)
+	for (i = 1; i < nbf; i++)
 	{
 		if (strcmp(header[i].name,name)==0)
 			value = header[i].value;
@@ -115,7 +134,7 @@ void changeValue(element_from_header* header, char* name, char* newValue)
 	int i;
 	int nbf = atoi(header[0].value);
 
-	for (i = 1; i <= nbf; i++)
+	for (i = 1; i < nbf; i++)
 	{
 		if (strcmp(header[i].name, name)==0)
 		{

libfasta/fasta_header_parser.c

@@ -798,7 +798,7 @@ YY_RULE_SETUP
 								(*p_header)[*nbf].value = (char*) malloc(sizeof(char)*size_needed);
 								strcpy(((*p_header)[*nbf]).value,header_yytext);
 										
-								(*nbf)++;
+								p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
 						  }
 	YY_BREAK
 case 3:
@@ -820,7 +820,7 @@ YY_RULE_SETUP
 case 5:
 YY_RULE_SETUP
 #line 69 "fasta_header_parser.l"
-{
+{  // TODO
 						/*fprintf(stderr,"\n<REGNAME>{SPACE} **%s**",header_yytext);*/
 						if (i != 0)
 							field = store_in_field(field,header_yytext,&free_size,&i);
@@ -886,24 +886,21 @@ case YY_STATE_EOF(REGVAL):
 #line 113 "fasta_header_parser.l"
 {
 					field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
-					p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
+                    (*nbf)++;
 					end_header_table(p_header, *nbf);
-					
 					free(field);
 					BEGIN(INITIAL);
                 	return 0;
                  }
 	YY_BREAK
 case YY_STATE_EOF(REGNAME):
-#line 123 "fasta_header_parser.l"
+#line 122 "fasta_header_parser.l"
 {
-						/*(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
-						strcpy((*p_header)[*nbf].name,"other_informations");
+						(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
+						strcpy((*p_header)[*nbf].name,"definition");
 						field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
-						p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);						
-						*/
-						end_header_table(p_header, *nbf);
-						
+                        (*nbf)++;
+						end_header_table(p_header, nbf);
 						free(field);
 						BEGIN(INITIAL);
 						return 0;
@@ -911,10 +908,10 @@ case YY_STATE_EOF(REGNAME):
 	YY_BREAK
 case 12:
 YY_RULE_SETUP
-#line 136 "fasta_header_parser.l"
+#line 133 "fasta_header_parser.l"
 ECHO;
 	YY_BREAK
-#line 918 "<stdout>"
+#line 915 "<stdout>"
 case YY_STATE_EOF(INITIAL):
 case YY_STATE_EOF(REGID):
 	yyterminate();
@@ -1912,7 +1909,7 @@ void header_yyfree (void * ptr )
 
 #define YYTABLES_NAME "yytables"
 
-#line 136 "fasta_header_parser.l"
+#line 133 "fasta_header_parser.l"
 
 
 
@@ -1923,38 +1920,32 @@ int header_yywrap()
 
 element_from_header* header_parser_main(char *h)
 {
-	int nbfields,memory_allocated;
+	int nbfields, memory_allocated;
 	element_from_header* header;
 	char* nbfields_n;
-	char* nbfields_v;
-	
-	nbfields_n = (char*) malloc(9*sizeof(char));
-	nbfields_v = (char*) malloc(5*sizeof(char));
+	YY_BUFFER_STATE state;
+    
+    state=header_yy_scan_string(h);
 	
 	memory_allocated=MEMALLOCATED;
 	
+    header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
+
+	nbfields_n = (char*) malloc(9*sizeof(char));
+	strcpy(nbfields_n, "nbfields");
+    header[0].name = nbfields_n;
+    
+    // Initialize memory to store the number of fields
+    header[0].value = (char*) malloc(10*sizeof(char));
+
 	nbfields=1;
 
-	strcpy(nbfields_n, "nbfields");
-	strcpy(nbfields_v, "1");
-
-    header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
-    
-    header[0].name = nbfields_n;
-    header[0].value = nbfields_v;
-    
-	YY_BUFFER_STATE state;
-
-	state=header_yy_scan_string(h);
-
     header_parser(&nbfields, &memory_allocated, &header);
-      
+    
     header_yy_delete_buffer(state);
-        
+    
     return header;
 }
 
 
 
-
-

libfasta/fasta_header_parser.l

@@ -53,7 +53,7 @@ EQUAL				=
 								(*p_header)[*nbf].value = (char*) malloc(sizeof(char)*size_needed);
 								strcpy(((*p_header)[*nbf]).value,yytext);
 										
-								(*nbf)++;
+								p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
 						  }
 
 
@@ -66,7 +66,7 @@ EQUAL				=
 						field = store_in_field(field,yytext,&free_size,&i);
 				    }
 
-<REGNAME>{SPACE}     {
+<REGNAME>{SPACE}     {  // TODO
 						/*fprintf(stderr,"\n<REGNAME>{SPACE} **%s**",yytext);*/
 						if (i != 0)
 							field = store_in_field(field,yytext,&free_size,&i);
@@ -112,22 +112,19 @@ EQUAL				=
 
 <REGVAL><<EOF>>  {
 					field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
-					p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
+                    (*nbf)++;
 					end_header_table(p_header, *nbf);
-					
 					free(field);
 					BEGIN(INITIAL);
                 	return 0;
                  }
 
 <REGNAME><<EOF>>      {
-						/*(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
-						strcpy((*p_header)[*nbf].name,"other_informations");
+						(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
+						strcpy((*p_header)[*nbf].name,"definition");
 						field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
-						p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);						
-						*/
-						end_header_table(p_header, *nbf);
-						
+                        (*nbf)++;
+						end_header_table(p_header, nbf);
 						free(field);
 						BEGIN(INITIAL);
 						return 0;
@@ -142,37 +139,31 @@ int header_yywrap()
 
 element_from_header* header_parser_main(char *h)
 {
-	int nbfields,memory_allocated;
+	int nbfields, memory_allocated;
 	element_from_header* header;
 	char* nbfields_n;
-	char* nbfields_v;
-	
-	nbfields_n = (char*) malloc(9*sizeof(char));
-	nbfields_v = (char*) malloc(5*sizeof(char));
+	YY_BUFFER_STATE state;
+    
+    state=yy_scan_string(h);
 	
 	memory_allocated=MEMALLOCATED;
 	
+    header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
+
+	nbfields_n = (char*) malloc(9*sizeof(char));
+	strcpy(nbfields_n, "nbfields");
+    header[0].name = nbfields_n;
+    
+    // Initialize memory to store the number of fields
+    header[0].value = (char*) malloc(10*sizeof(char));
+
 	nbfields=1;
 
-	strcpy(nbfields_n, "nbfields");
-	strcpy(nbfields_v, "1");
-
-    header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
-    
-    header[0].name = nbfields_n;
-    header[0].value = nbfields_v;
-    
-	YY_BUFFER_STATE state;
-
-	state=yy_scan_string(h);
-
     header_parser(&nbfields, &memory_allocated, &header);
-      
+    
     yy_delete_buffer(state);
-        
+    
     return header;
 }
 
 
-
-

libfasta/fasta_seq_writer.c

@@ -52,7 +52,7 @@ void printOnlyHeaderFromTable(element_from_header* header, FILE* output)
 
 	fprintf(output,">%s ",header[1].value);
 
-	for (i = 2; i <= nbf; i++)
+	for (i = 2; i < nbf; i++)
 	{
 		if (strcmp(header[i].name, "definition") != 0)
 		{
@@ -60,11 +60,10 @@ void printOnlyHeaderFromTable(element_from_header* header, FILE* output)
 			fprintf(output,"=");
 		    fprintf(output,"%s; ",header[i].value);
 		}
+		else if (strcmp(header[i].name, "definition") == 0)
+			fprintf(output,"%s ", header[i].value);
 	}
 
-	if (strcmp(header[nbf].name, "definition") == 0)
-		fprintf(output,"%s; ",header[nbf].value);
-
 	fprintf(output,"\n");
 }
 

libfasta/header_mem_handler.c

@@ -76,7 +76,7 @@ element_from_header** check_and_realloc_mem_in_header_table(element_from_header*
 {
 	(*nbf)++;
 
-	if (*nbf == *memory_allocated)
+	if ((*nbf)+1 == *memory_allocated)
 	{
 		(*memory_allocated)++;
 		*p_header = (element_from_header*) realloc(*p_header, (*memory_allocated) * sizeof(element_from_header));
@@ -87,7 +87,6 @@ element_from_header** check_and_realloc_mem_in_header_table(element_from_header*
 
 void end_header_table(element_from_header** p_header, int nbf)
 {
-	nbf = nbf - 1;
-	//fprintf(stderr, "nbf = %d", nbf);
+	*p_header = (element_from_header*) realloc(*p_header, nbf * sizeof(element_from_header));
 	sprintf((*p_header)->value, "%d", nbf);
 }

liblcs/sse_banded_LCS_alignment.c

@@ -458,6 +458,9 @@ int calculateSizeToAllocate(int maxLen, int minLen, int LCSmin)
 
 	calculateBandLengths(maxLen, minLen, &notUsed, &size, LCSmin);		// max size = max left band length * 2
 
+	if (!size)	// Happens if there is no threshold (threshold is 100% similarity) and generates bugs if left to 0
+		size = 1;
+
 	//fprintf(stderr, "\nsize for address before %8 = %d", size);
 
 	size*= 2;