[med-svn] r10537 - in trunk/packages/bowtie/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2012-04-23 09:10:37 +0000 (Mon, 23 Apr 2012)
New Revision: 10537

Added:
   trunk/packages/bowtie/trunk/debian/patches/gcc-4.7.patch
   trunk/packages/bowtie/trunk/debian/patches/series
Modified:
   trunk/packages/bowtie/trunk/debian/changelog
Log:
Patch to build using gcc-4.7


Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog	2012-04-23 08:34:52 UTC (rev 10536)
+++ trunk/packages/bowtie/trunk/debian/changelog	2012-04-23 09:10:37 UTC (rev 10537)
@@ -8,6 +8,11 @@
   * debian/rules: calculate pkg name instead of setting it
   * debian/copyright: DEP5 verified using
      cme fix dpkg-copyright
+  * debian/patches/gcc-4.7.patch: function "reverseInPlace" is declared after
+    the function is used
+    Thanks to Rodolfo García Peñas <kix at kix.es> and
+    gregor herrmann <gregoa at debian.org>
+    Closes: #667120
 
  -- Andreas Tille <tille at debian.org>  Sun, 22 Apr 2012 21:09:05 +0200
 

Added: trunk/packages/bowtie/trunk/debian/patches/gcc-4.7.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/gcc-4.7.patch	                        (rev 0)
+++ trunk/packages/bowtie/trunk/debian/patches/gcc-4.7.patch	2012-04-23 09:10:37 UTC (rev 10537)
@@ -0,0 +1,49 @@
+Author: gregor herrmann <gregoa at debian.org>,
+Date: Sun, 22 Apr 2012 22:27:51 +0200
+Bug-Closed: http://bugs.debian.org/667120
+Description: function "reverseInPlace" is declared after the function is used
+ For more detailed information see
+   http://lists.debian.org/debian-mentors/2012/04/msg00409.html
+ and other mails in this thread.
+
+--- bowtie-0.12.7.orig/alphabet.h
++++ bowtie-0.12.7/alphabet.h
+@@ -41,6 +41,19 @@
+ /**
+  * Reverse-complement s in-place.  Ns go to Ns.
+  */
++
++/// 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;
++	}
++}
++
+ template<typename TStr>
+ static inline void reverseComplementInPlace(TStr& s, bool color) {
+ 	typedef typename Value<TStr>::Type TVal;
+@@ -69,18 +82,6 @@
+ 	}
+ }
+ 
+-/// 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.
+  */

Added: trunk/packages/bowtie/trunk/debian/patches/series
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/bowtie/trunk/debian/patches/series	2012-04-23 09:10:37 UTC (rev 10537)
@@ -0,0 +1 @@
+gcc-4.7.patch