[med-svn] [sniffles] 04/07: refresh patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository sniffles.

commit 504cf4daf5d3d3a84388a7300af35ad3ebda03cc
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jan 13 15:05:21 2017 +0100

    refresh patches
---
 debian/patches/external-libs.patch   | 12 ++++++------
 debian/patches/no-extra-binary.patch | 12 +++++++-----
 2 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
index ae856cb..3b4482a 100644
--- a/debian/patches/external-libs.patch
+++ b/debian/patches/external-libs.patch
@@ -3,9 +3,9 @@ Author: Afif Elghraoui <afif at debian.org>
 Forwarded: not-needed
 Last-Update: 2016-06-18
 
---- sniffles.orig/CMakeLists.txt
-+++ sniffles/CMakeLists.txt
-@@ -30,7 +30,5 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -30,7 +30,5 @@ if(OPENMP_FOUND)
  endif()
  
  
@@ -13,8 +13,8 @@ Last-Update: 2016-06-18
 -add_subdirectory(lib/bamtools-2.3.0)
  
  add_subdirectory(src)
---- sniffles.orig/src/CMakeLists.txt
-+++ sniffles/src/CMakeLists.txt
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
 @@ -1,6 +1,8 @@
  cmake_minimum_required(VERSION 2.8)
  project(Sniffles)
@@ -24,7 +24,7 @@ Last-Update: 2016-06-18
  include_directories (../lib/bamtools-2.3.0/src)
  include_directories(../lib/tclap-1.2.1/include)
  
-@@ -29,8 +31,8 @@
+@@ -30,8 +32,8 @@ add_executable(sniffles
  					)										
  					
  #target_link_libraries(ngm-core pthread)	
diff --git a/debian/patches/no-extra-binary.patch b/debian/patches/no-extra-binary.patch
index 0c1f312..12139f8 100644
--- a/debian/patches/no-extra-binary.patch
+++ b/debian/patches/no-extra-binary.patch
@@ -4,12 +4,13 @@ Description: Do not build <target>-debug programs
 Author: Afif Elghraoui <afif at debian.org>
 Forwarded: not-needed
 Last-Update: 2016-06-18
---- sniffles.orig/src/CMakeLists.txt
-+++ sniffles/src/CMakeLists.txt
-@@ -34,31 +34,3 @@
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -34,33 +34,4 @@ add_executable(sniffles
+ #target_link_libraries(ngm-core pthread)	
  TARGET_LINK_LIBRARIES(sniffles bamtools)
  TARGET_LINK_LIBRARIES(sniffles z)
- 	
+-	
 -add_executable(sniffles-debug 	
 -                    tree/Breakpoint_Tree.cpp
 -                    Genotyper/Genotyper.cpp
@@ -18,6 +19,7 @@ Last-Update: 2016-06-18
 -					Sniffles.cpp
 -					Ignore_Regions.cpp
 -					tree/Intervall_bed.cpp
+-					tree/IntervallList.cpp
 -					sub/Detect_Breakpoints.cpp
 -					sub/Breakpoint.cpp
 -					tree/IntervallTree.cpp
@@ -37,4 +39,4 @@ Last-Update: 2016-06-18
 -#target_link_libraries(sniffles-debug pthread)
 -TARGET_LINK_LIBRARIES(sniffles-debug BamTools-static)
 -TARGET_LINK_LIBRARIES(sniffles-debug zlibstatic)
--
+ 

-- 
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