Temporarily switching back to older bugless fasta libs while fixing a

bug

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"
 {
@@ -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"
 {
@@ -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"
 {
@@ -911,7 +914,7 @@ YY_RULE_SETUP
 #line 136 "fasta_header_parser.l"
 ECHO;
 	YY_BREAK
-#line 915 "<stdout>"
+#line 918 "<stdout>"
 case YY_STATE_EOF(INITIAL):
 case YY_STATE_EOF(REGID):
 	yyterminate();
@@ -1105,7 +1108,7 @@ 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 +1241,7 @@ 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 +1329,7 @@ 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 +1465,10 @@ 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 +1673,8 @@ 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 +1682,7 @@ 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;

libfasta/fasta_header_parser.l

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

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;