[med-svn] r16400 - in trunk/packages/bowtie/trunk/debian: . patches

[Ognyan Kulev]

Author: ogi
Date: 2014-03-08 14:02:19 +0000 (Sat, 08 Mar 2014)
New Revision: 16400

Added:
   trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch
Modified:
   trunk/packages/bowtie/trunk/debian/changelog
   trunk/packages/bowtie/trunk/debian/control
   trunk/packages/bowtie/trunk/debian/patches/series
Log:
New patch debian/patches/seqan-popcount.patch. SeqAn 1.4 is required. Standards-Version: 3.9.5. Updated Vcs-Svn and Vcs-Browse.



Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog	2014-03-07 11:15:12 UTC (rev 16399)
+++ trunk/packages/bowtie/trunk/debian/changelog	2014-03-08 14:02:19 UTC (rev 16400)
@@ -1,3 +1,12 @@
+bowtie (1.0.0-6) unstable; urgency=low
+
+  * debian/patches/seqan-popcount.patch: New patch.
+  * Version 1.4 of seqan-dev is required now.
+  * Standards-Version: 3.9.5 (no changes needed).
+  * Updated Vcs-Svn and Vcs-Browse fields as per Debian-Med policy.
+
+ -- Ognyan Kulev <ogi at debian.org>  Sat, 08 Mar 2014 15:13:16 +0200
+
 bowtie (1.0.0-5) unstable; urgency=low
 
   * Fixed (hopefully) FTBFS by using override_dh_fixperms-indep target

Modified: trunk/packages/bowtie/trunk/debian/control
===================================================================
--- trunk/packages/bowtie/trunk/debian/control	2014-03-07 11:15:12 UTC (rev 16399)
+++ trunk/packages/bowtie/trunk/debian/control	2014-03-08 14:02:19 UTC (rev 16400)
@@ -6,11 +6,11 @@
  Yask Gupta <yask.gupta87 at gmail.com>,
  Andreas Tille <tille at debian.org>,
  Ognyan Kulev <ogi at debian.org>
-Build-Depends: debhelper (>= 9), help2man, seqan-dev (>= 1.3)
-Standards-Version: 3.9.4
+Build-Depends: debhelper (>= 9), help2man, seqan-dev (>= 1.4)
+Standards-Version: 3.9.5
 Homepage: http://bowtie-bio.sourceforge.net/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bowtie/trunk
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bowtie/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bowtie/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bowtie/trunk/
 
 Package: bowtie
 Architecture: any

Added: trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch	                        (rev 0)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch	2014-03-08 14:02:19 UTC (rev 16400)
@@ -0,0 +1,24 @@
+Description: Use SeqAn 1.4's seqan::popCount() function instead of own function
+Author: Ognyan Kulev <ogi at debian.org>
+Last-Update: 2014-03-08
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bowtie-1.0.0.orig/diff_sample.h
++++ bowtie-1.0.0/diff_sample.h
+@@ -475,6 +475,8 @@
+ 	return amap;
+ }
+ 
++// Debian: Use seqan::popCount
++#if 0
+ /**
+  * Return population count (count of all bits set to 1) of i.
+  */
+@@ -487,6 +489,7 @@
+ 	}
+ 	return cnt;
+ }
++#endif
+ 
+ /**
+  * Calculate log-base-2 of i

Modified: trunk/packages/bowtie/trunk/debian/patches/series
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/series	2014-03-07 11:15:12 UTC (rev 16399)
+++ trunk/packages/bowtie/trunk/debian/patches/series	2014-03-08 14:02:19 UTC (rev 16400)
@@ -5,3 +5,4 @@
 seqan-rename-fill-to-resize.patch
 disable_bits_flag.patch
 no_hash_style_both_for_mips.patch
+seqan-popcount.patch