--- bowtie-0.12.7/alphabet.h	2009-11-24 20:53:52.000000000 +0000

+++ bowtie-0.12.7.new/alphabet.h	2012-01-09 10:53:09.902974406 +0000

@@ -38,6 +38,18 @@

 	return s_rc;

 }

+/// Reverse a string in-place

+template <typename TStr>

+static inline void reverseInPlace(TStr& s) {

+	typedef typename Value<TStr>::Type TVal;

+	size_t len = length(s);

+	for(size_t i = 0; i < (len>>1); i++) {

+		TVal tmp = s[i];

+		s[i] = s[len-i-1];

+		s[len-i-1] = tmp;

+	}

+}

+

 /**

  * Reverse-complement s in-place.  Ns go to Ns.

  */

@@ -69,17 +81,6 @@

 	}

 }

-/// Reverse a string in-place

-template <typename TStr>

-static inline void reverseInPlace(TStr& s) {

-	typedef typename Value<TStr>::Type TVal;

-	size_t len = length(s);

-	for(size_t i = 0; i < (len>>1); i++) {

-		TVal tmp = s[i];

-		s[i] = s[len-i-1];

-		s[len-i-1] = tmp;

-	}

-}

 /**

  * Return the reverse-complement of s.