[med-svn] [sniffles] 03/04: Update patches

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository sniffles.

commit 8699b462d1c5b7ea9181925684e0ec9a1e0bd1fc
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Nov 23 01:34:27 2017 -0500

    Update patches
---
 debian/patches/external-libs.patch   | 12 ++++++------
 debian/patches/no-extra-binary.patch |  8 +++++---
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
index 3b4482a..c154dc5 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
 
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -30,7 +30,5 @@ if(OPENMP_FOUND)
+--- sniffles.orig/CMakeLists.txt
++++ sniffles/CMakeLists.txt
+@@ -30,7 +30,5 @@
  endif()
  
  
@@ -13,8 +13,8 @@ Last-Update: 2016-06-18
 -add_subdirectory(lib/bamtools-2.3.0)
  
  add_subdirectory(src)
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
+--- sniffles.orig/src/CMakeLists.txt
++++ sniffles/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)
  
-@@ -30,8 +32,8 @@ add_executable(sniffles
+@@ -32,8 +34,8 @@
  					)										
  					
  #target_link_libraries(ngm-core pthread)	
diff --git a/debian/patches/no-extra-binary.patch b/debian/patches/no-extra-binary.patch
index 12139f8..dabda76 100644
--- a/debian/patches/no-extra-binary.patch
+++ b/debian/patches/no-extra-binary.patch
@@ -4,9 +4,9 @@ Description: Do not build <target>-debug programs
 Author: Afif Elghraoui <afif at debian.org>
 Forwarded: not-needed
 Last-Update: 2016-06-18
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -34,33 +34,4 @@ add_executable(sniffles
+--- sniffles.orig/src/CMakeLists.txt
++++ sniffles/src/CMakeLists.txt
+@@ -36,35 +36,4 @@
  #target_link_libraries(ngm-core pthread)	
  TARGET_LINK_LIBRARIES(sniffles bamtools)
  TARGET_LINK_LIBRARIES(sniffles z)
@@ -32,6 +32,8 @@ Last-Update: 2016-06-18
 -					print/NGMPrinter.cpp
 -					plane-sweep/PlaneSweep_slim.cpp
 -					cluster/Cluster_SVs.cpp
+-					force_calling/Force_calling.cpp
+-					force_calling/VCF_parser.cpp
 -					)	
 -
 -SET_TARGET_PROPERTIES(sniffles-debug PROPERTIES COMPILE_FLAGS "-g3 -O0")

-- 
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