Implemented functions to build reverse complement sequences

src/utils.h

@@ -20,10 +20,16 @@
 #include "obitypes.h"
 
 
-#define FORMATTED_TIME_LENGTH (1024)    /**< The length allocated for the character string containing a formatted date.
- 	 	 	 	 	 	 	 	 	     */
-#define ONE_IF_ZERO(x) (((x)==0)?1:(x))	/**< If x is equal to 0, x takes the value 1.
-                                	   	 */
+#define FORMATTED_TIME_LENGTH (1024)    					/**< The length allocated for the character string containing a formatted date.
+ 	 	 	 	 	 	 	 	 	     	 	 	 	 	 */
+#define ONE_IF_ZERO(x) (((x)==0)?1:(x))						/**< If x is equal to 0, x takes the value 1.
+                                	   	 	 	 	 	 	 */
+#define DNA_ALPHA   "acgtbdefhijklmnopqrsuvwxyz#![]"	    /**< DNA alphabet (IUPAC).
+ 	 	 	 	  //"ABCDEFGHIJKLMNOPQRSTUVWXYZ#![]" 	 	 */
+#define CDNA_ALPHA  "tgcavhefdijmlknopqysabwxrz#!]["		/**< Complementary DNA alphabet (IUPAC).
+ 	 	 	 	  //"TVGHEFCDIJMLKNOPQYSAABWXRZ#!][" 	 	 */
+
+
 
 /**
  * @brief Copy the content of a file into another file.
@@ -155,4 +161,38 @@ void* bsearch_user_data(const void* key, const void* base, size_t num, size_t si
 void qsort_user_data(void *aa, size_t n, size_t es, const void *user_data, int (*cmp)(const void *, const void *, const void *));
 
 
+/**
+ * Function returning the reverse complement of a nucleotide sequence.
+ *
+ * @warning The sequence must be in lower case.
+ * @warning The sequence will be replaced by its reverse complement without being copied.
+ *
+ * @param nucAcSeq The nucleotide sequence.
+ *
+ * @returns The reverse complemented sequence.
+ *
+ * @since December 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @note Copied from ecoPCR source code
+ */
+char* reverse_complement_sequence(char* nucAcSeq);
+
+
+/**
+ * Function returning the reverse complement of a pattern.
+ *
+ * @warning The pattern must be in lower case.
+ * @warning The pattern will be replaced by its reverse complement without being copied.
+ *
+ * @param nucAcSeq The pattern.
+ *
+ * @returns The reverse complemented pattern.
+ *
+ * @since December 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @note Copied from ecoPCR source code
+ */
+char* reverse_complement_pattern(char* nucAcSeq);
+
+
 #endif /* UTILS_H_ */