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tille pushed a commit to branch master
in repository tvc.
commit 381c43ebada2d7a34bce11459f5b0694f53e0100
Author: Andreas Tille <ti...@debian.org>
Date: Fri Jan 13 13:45:11 2017 +0100
Add libraries that are missing from cmake file but needed when using Debian
packaged cvflib
---
debian/patches/use_debian_packaged_vcflib.patch | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/debian/patches/use_debian_packaged_vcflib.patch
b/debian/patches/use_debian_packaged_vcflib.patch
index 0786be9..bc4648b 100644
--- a/debian/patches/use_debian_packaged_vcflib.patch
+++ b/debian/patches/use_debian_packaged_vcflib.patch
@@ -1,6 +1,6 @@
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -18,10 +18,9 @@ configure_file (
+@@ -18,10 +18,10 @@ configure_file (
)
@@ -8,11 +8,12 @@
set(ION_FREEBAYES_DIR external/freebayes)
-include_directories(${ION_VCFLIB_DIR})
++include_directories("/usr/include/smithwaterman")
+include_directories("/usr/include/vcflib")
include_directories(${ION_FREEBAYES_DIR}/src)
include_directories("/usr/include/jsoncpp")
-@@ -78,17 +77,6 @@ set(tvcSRCS
+@@ -78,17 +78,6 @@ set(tvcSRCS
VariantCaller/EnsembleEval/StackEngine.cpp
VariantCaller/EnsembleEval/CrossHypotheses.cpp
@@ -30,16 +31,16 @@
${ION_FREEBAYES_DIR}/src/AlleleParser.cpp
BaseCaller/PIDloop.cpp
-@@ -120,7 +108,7 @@ add_executable(tvcassembly
+@@ -120,7 +109,7 @@ add_executable(tvcassembly
${PROJECT_BINARY_DIR}/IonVersion.cpp
)
-target_link_libraries(tvcassembly bamtools z pthread jsoncpp)
-+target_link_libraries(tvcassembly bamtools z pthread jsoncpp vcflib)
++target_link_libraries(tvcassembly bamtools z pthread jsoncpp tabixpp
smithwaterman vcflib)
add_executable(tvcutils
-@@ -130,15 +118,6 @@ add_executable(tvcutils
+@@ -130,15 +119,6 @@ add_executable(tvcutils
VariantCaller/tvcutils/unify_vcf.cpp
VariantCaller/TargetsManager.cpp
Util/OptArgs.cpp
--
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