[med-svn] [sniffles] 03/06: Update patches

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository sniffles.

commit dd60865b46f2c4f7e4c72fcc57d621ed6d13def2
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Oct 17 01:31:00 2016 -0700

    Update patches
---
 debian/patches/external-libs.patch   |  4 ++--
 debian/patches/no-extra-binary.patch | 11 ++++++-----
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
index 53ad912..ae856cb 100644
--- a/debian/patches/external-libs.patch
+++ b/debian/patches/external-libs.patch
@@ -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)
  
-@@ -28,8 +30,8 @@
+@@ -29,8 +31,8 @@
  					)										
  					
  #target_link_libraries(ngm-core pthread)	
@@ -34,4 +34,4 @@ Last-Update: 2016-06-18
 +TARGET_LINK_LIBRARIES(sniffles z)
  	
  add_executable(sniffles-debug 	
- 					Alignment.cpp
+                     tree/Breakpoint_Tree.cpp
diff --git a/debian/patches/no-extra-binary.patch b/debian/patches/no-extra-binary.patch
index abadd97..0c1f312 100644
--- a/debian/patches/no-extra-binary.patch
+++ b/debian/patches/no-extra-binary.patch
@@ -6,14 +6,15 @@ Forwarded: not-needed
 Last-Update: 2016-06-18
 --- sniffles.orig/src/CMakeLists.txt
 +++ sniffles/src/CMakeLists.txt
-@@ -33,30 +33,3 @@
+@@ -34,31 +34,3 @@
  TARGET_LINK_LIBRARIES(sniffles bamtools)
  TARGET_LINK_LIBRARIES(sniffles z)
  	
 -add_executable(sniffles-debug 	
+-                    tree/Breakpoint_Tree.cpp
+-                    Genotyper/Genotyper.cpp
 -					Alignment.cpp
 -					BamParser.cpp
--					Parser.cpp
 -					Sniffles.cpp
 -					Ignore_Regions.cpp
 -					tree/Intervall_bed.cpp
@@ -23,12 +24,12 @@ Last-Update: 2016-06-18
 -					realign/SWCPU.cpp
 -					realign/Realign.cpp
 -					print/VCFPrinter.cpp
--					print/BedePrinter.cpp
--					print/MariaPrinter.cpp
+-					print/BedpePrinter.cpp
 -					print/IPrinter.cpp
--					phasing/PhaserSV.cpp
 -					tree/BinTree.cpp
 -					print/NGMPrinter.cpp
+-					plane-sweep/PlaneSweep_slim.cpp
+-					cluster/Cluster_SVs.cpp
 -					)	
 -
 -SET_TARGET_PROPERTIES(sniffles-debug PROPERTIES COMPILE_FLAGS "-g3 -O0")

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