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

@@ -27,7 +27,7 @@
 #define FLEX_SCANNER
 #define YY_FLEX_MAJOR_VERSION 2
 #define YY_FLEX_MINOR_VERSION 5
-#define YY_FLEX_SUBMINOR_VERSION 37
+#define YY_FLEX_SUBMINOR_VERSION 35
 #if YY_FLEX_SUBMINOR_VERSION > 0
 #define FLEX_BETA
 #endif
@@ -65,6 +65,7 @@ typedef int16_t flex_int16_t;
 typedef uint16_t flex_uint16_t;
 typedef int32_t flex_int32_t;
 typedef uint32_t flex_uint32_t;
+typedef uint64_t flex_uint64_t;
 #else
 typedef signed char flex_int8_t;
 typedef short int flex_int16_t;
@@ -72,6 +73,7 @@ typedef int flex_int32_t;
 typedef unsigned char flex_uint8_t; 
 typedef unsigned short int flex_uint16_t;
 typedef unsigned int flex_uint32_t;
+#endif /* ! C99 */
 
 /* Limits of integral types. */
 #ifndef INT8_MIN
@@ -102,8 +104,6 @@ typedef unsigned int flex_uint32_t;
 #define UINT32_MAX             (4294967295U)
 #endif
 
-#endif /* ! C99 */
-
 #endif /* ! FLEXINT_H */
 
 #ifdef __cplusplus
@@ -374,7 +374,7 @@ static void yy_fatal_error (yyconst char msg[]  );
  */
 #define YY_DO_BEFORE_ACTION \
 	(yytext_ptr) = yy_bp; \
-	header_yyleng = (size_t) (yy_cp - yy_bp); \
+	header_yyleng = (yy_size_t) (yy_cp - yy_bp); \
 	(yy_hold_char) = *yy_cp; \
 	*yy_cp = '\0'; \
 	(yy_c_buf_p) = yy_cp;
@@ -390,9 +390,9 @@ struct yy_trans_info
 	};
 static yyconst flex_int16_t yy_accept[29] =
     {   0,
-        0,    0,    0,    0,    0,    0,    0,    0,   13,   12,
-        3,    2,    1,    5,    4,    7,    6,    9,    8,   10,
-       11,    3,    2,    5,    4,    9,    8,    0
+        0,    0,    0,    0,    0,    0,    0,    0,   13,    2,
+        3,    1,   12,    4,    5,    7,    6,    8,    9,   10,
+       11,    2,    3,    4,    5,    8,    9,    0
     } ;
 
 static yyconst flex_int32_t yy_ec[256] =
@@ -400,17 +400,17 @@ static yyconst flex_int32_t yy_ec[256] =
         1,    1,    1,    1,    1,    1,    1,    1,    2,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
-        1,    2,    1,    3,    3,    1,    3,    3,    3,    3,
-        3,    1,    3,    3,    3,    3,    3,    3,    3,    3,
-        3,    3,    3,    3,    3,    3,    3,    3,    4,    1,
-        5,    6,    1,    1,    3,    3,    3,    3,    3,    3,
-        3,    3,    3,    3,    3,    3,    3,    3,    3,    3,
-        3,    3,    3,    3,    3,    3,    3,    3,    3,    3,
-        3,    1,    3,    1,    3,    1,    3,    3,    3,    3,
+        1,    2,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    3,    1,
+        4,    5,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
 
-        3,    3,    3,    3,    3,    3,    3,    3,    3,    3,
-        3,    3,    3,    3,    3,    3,    3,    3,    3,    3,
-        3,    3,    3,    3,    3,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
         1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
@@ -427,41 +427,41 @@ static yyconst flex_int32_t yy_ec[256] =
         1,    1,    1,    1,    1
     } ;
 
-static yyconst flex_int32_t yy_meta[7] =
+static yyconst flex_int32_t yy_meta[6] =
     {   0,
-        1,    2,    3,    4,    4,    1
+        1,    2,    3,    3,    4
     } ;
 
-static yyconst flex_int16_t yy_base[35] =
+static yyconst flex_int16_t yy_base[36] =
     {   0,
-        0,    0,   22,   21,    6,    0,   12,    0,   26,   29,
-        0,    0,   29,    0,    0,   29,   29,    0,    0,   29,
-       29,    0,    0,    0,    0,    0,    0,   29,   23,   16,
-       22,   20,   20,   18
+        0,    4,   23,    0,    9,    0,   14,    0,   27,    0,
+        0,   29,   29,    0,    0,   29,   29,    0,    0,   29,
+       29,    0,    0,    0,    0,    0,    0,   29,   19,   23,
+       23,    7,    5,    3,    1
     } ;
 
-static yyconst flex_int16_t yy_def[35] =
+static yyconst flex_int16_t yy_def[36] =
     {   0,
-       28,    1,    1,    1,   28,    5,   28,    7,   28,   28,
-       29,   30,   28,   31,   32,   28,   28,   33,   34,   28,
-       28,   29,   30,   31,   32,   33,   34,    0,   28,   28,
+       29,   29,    2,    3,   28,    5,   28,    7,   28,   30,
+       31,   28,   28,   32,   33,   28,   28,   34,   35,   28,
+       28,   30,   31,   32,   33,   34,   35,    0,   28,   28,
+       28,   28,   28,   28,   28
+    } ;
+
+static yyconst flex_int16_t yy_nxt[35] =
+    {   0,
+       28,   11,   27,   26,   12,   11,   25,   24,   12,   14,
+       15,   16,   17,   13,   18,   19,   20,   21,   13,   10,
+       10,   10,   10,   22,   23,   22,   28,   13,    9,   28,
        28,   28,   28,   28
     } ;
 
-static yyconst flex_int16_t yy_nxt[36] =
+static yyconst flex_int16_t yy_chk[35] =
     {   0,
-       10,   11,   12,   12,   12,   13,   10,   14,   15,   16,
-       17,   10,   10,   18,   19,   20,   21,   10,   23,   23,
-       27,   26,   25,   24,   22,   28,   10,   10,    9,   28,
-       28,   28,   28,   28,   28
-    } ;
-
-static yyconst flex_int16_t yy_chk[36] =
-    {   0,
-        1,    1,    1,    1,    1,    1,    5,    5,    5,    5,
-        5,    5,    7,    7,    7,    7,    7,    7,   30,   30,
-       34,   33,   32,   31,   29,    9,    4,    3,   28,   28,
-       28,   28,   28,   28,   28
+        0,    1,   35,   34,    1,    2,   33,   32,    2,    5,
+        5,    5,    5,    5,    7,    7,    7,    7,    7,   29,
+       29,   29,   29,   30,   31,   30,    9,    3,   28,   28,
+       28,   28,   28,   28
     } ;
 
 static yy_state_type yy_last_accepting_state;
@@ -590,7 +590,7 @@ static int input (void );
 /* This used to be an fputs(), but since the string might contain NUL's,
  * we now use fwrite().
  */
-#define ECHO do { if (fwrite( header_yytext, header_yyleng, 1, header_yyout )) {} } while (0)
+#define ECHO fwrite( header_yytext, header_yyleng, 1, header_yyout )
 #endif
 
 /* Gets input and stuffs it into "buf".  number of characters read, or YY_NULL,
@@ -601,7 +601,7 @@ static int input (void );
 	if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \
 		{ \
 		int c = '*'; \
-		size_t n; \
+		yy_size_t n; \
 		for ( n = 0; n < max_size && \
 			     (c = getc( header_yyin )) != EOF && c != '\n'; ++n ) \
 			buf[n] = (char) c; \
@@ -784,6 +784,7 @@ YY_RULE_SETUP
 				}
 	YY_BREAK
 case 2:
+/* rule 2 can match eol */
 YY_RULE_SETUP
 #line 45 "fasta_header_parser.l"
 {
@@ -797,7 +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:
@@ -808,6 +809,7 @@ YY_RULE_SETUP
 					}
 	YY_BREAK
 case 4:
+/* rule 4 can match eol */
 YY_RULE_SETUP
 #line 64 "fasta_header_parser.l"
 {
@@ -818,7 +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);
@@ -846,6 +848,7 @@ YY_RULE_SETUP
 				    }
 	YY_BREAK
 case 8:
+/* rule 8 can match eol */
 YY_RULE_SETUP
 #line 90 "fasta_header_parser.l"
 {
@@ -883,24 +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;
@@ -908,7 +908,7 @@ 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 915 "<stdout>"
@@ -1105,7 +1105,7 @@ static int yy_get_next_buffer (void)
 			{ /* Not enough room in the buffer - grow it. */
 
 			/* just a shorter name for the current buffer */
-			YY_BUFFER_STATE b = YY_CURRENT_BUFFER_LVALUE;
+			YY_BUFFER_STATE b = YY_CURRENT_BUFFER;
 
 			int yy_c_buf_p_offset =
 				(int) ((yy_c_buf_p) - b->yy_ch_buf);
@@ -1238,7 +1238,7 @@ static int yy_get_next_buffer (void)
 	yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c];
 	yy_is_jam = (yy_current_state == 28);
 
-		return yy_is_jam ? 0 : yy_current_state;
+	return yy_is_jam ? 0 : yy_current_state;
 }
 
     static void yyunput (int c, register char * yy_bp )
@@ -1326,7 +1326,7 @@ static int yy_get_next_buffer (void)
 				case EOB_ACT_END_OF_FILE:
 					{
 					if ( header_yywrap( ) )
-						return EOF;
+						return 0;
 
 					if ( ! (yy_did_buffer_switch_on_eof) )
 						YY_NEW_FILE;
@@ -1462,6 +1462,10 @@ static void header_yy_load_buffer_state  (void)
 	header_yyfree((void *) b  );
 }
 
+#ifndef __cplusplus
+extern int isatty (int );
+#endif /* __cplusplus */
+    
 /* Initializes or reinitializes a buffer.
  * This function is sometimes called more than once on the same buffer,
  * such as during a header_yyrestart() or at EOF.
@@ -1666,8 +1670,8 @@ YY_BUFFER_STATE header_yy_scan_string (yyconst char * yystr )
 
 /** Setup the input buffer state to scan the given bytes. The next call to header_yylex() will
  * scan from a @e copy of @a bytes.
- * @param yybytes the byte buffer to scan
- * @param _yybytes_len the number of bytes in the buffer pointed to by @a bytes.
+ * @param bytes the byte buffer to scan
+ * @param len the number of bytes in the buffer pointed to by @a bytes.
  * 
  * @return the newly allocated buffer state object.
  */
@@ -1675,8 +1679,7 @@ YY_BUFFER_STATE header_yy_scan_bytes  (yyconst char * yybytes, yy_size_t  _yybyt
 {
 	YY_BUFFER_STATE b;
 	char *buf;
-	yy_size_t n;
-	int i;
+	yy_size_t n, i;
     
 	/* Get memory for full buffer, including space for trailing EOB's. */
 	n = _yybytes_len + 2;
@@ -1906,7 +1909,7 @@ void header_yyfree (void * ptr )
 
 #define YYTABLES_NAME "yytables"
 
-#line 136 "fasta_header_parser.l"
+#line 133 "fasta_header_parser.l"
 
 
 
@@ -1917,38 +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

@@ -21,8 +21,8 @@
 	
 %}
 
-WORD				[[:alnum:]:\-.{},'_()\#\[\]\|\&\"\'\/\%\+]+
-WORDID				[[:alnum:]:\-.{},'_()\#\[\]\|\&\"\'\/\%\+=;]+
+WORD                [^>[:blank:]=;]+
+WORDID              [^>[:blank:]]+
 SUP					>
 EOL                	\n
 SEP                 ;
@@ -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);
 }

libfasta/sequence.c

@@ -223,7 +223,13 @@ fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC)
     fastaSeqCount allseqs;
     int32_t discarded=0;
 
-    fp = file_open(fileName, TRUE);
+    if ((fileName == NULL) || (strcmp(fileName, "-") == 0))
+    	fp = stdin;
+    else
+    {
+    	fp = file_open(fileName, TRUE);
+    	exitIfEmptyFile(fp);
+    }
 
     if (fp == NULL)
     {
@@ -231,8 +237,6 @@ fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC)
             exit(1);
     }
 
-    exitIfEmptyFile(fp);
-
     seqPtrAr = (fastaSeqPtr) util_malloc(slots*sizeof(fastaSeq), __FILE__, __LINE__);
 
     seqPtr = seq_getNext(fp, " ", isStandardSeq, onlyATGC);

libfile/fileHandling.c

@@ -44,7 +44,7 @@ FILE *file_openrw(char* fileName, BOOL abortOnError)
 
 /*
  * Function Name: fileNextChar(FILE* fp)
- * Description:   Reads the file and returns next character, if file is null or its end of file, returns \<5C>.
+ * Description:   Reads the file and returns next character, if file is null or its end of file, returns \<5C>.
  */
 char file_nextChar(FILE* fp)
 {
@@ -59,7 +59,7 @@ char file_nextChar(FILE* fp)
 
 /*
  * Function Name: *fileNextLine(FILE *fp, char *buffer, int32_t bufferSize)
- * Description:   Reads the file and returns next line, if file is null or its end of file, returns \<5C>.
+ * Description:   Reads the file and returns next line, if file is null or its end of file, returns \<5C>.
  */
 char *file_nextLine(FILE *fp, char *buffer, int32_t bufferSize)
 {
@@ -76,7 +76,11 @@ char *file_nextLine(FILE *fp, char *buffer, int32_t bufferSize)
 void exitIfEmptyFile(FILE *file)
 {
     long savedOffset = ftell(file);
-    fseek(file, 0, SEEK_END);
+    if (fseek(file, 0, SEEK_END) != 0)
+    {
+        fprintf(stderr, "\nError moving the offset in an input file\n");
+        exit(1);
+    }
 
     if (ftell(file) == 0)
     {

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;