[med-svn] [tvc] 05/05: Add libraries that are missing from cmake file but needed when using Debian packaged cvflib

[Andreas Tille]

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tille pushed a commit to branch master
in repository tvc.

commit 381c43ebada2d7a34bce11459f5b0694f53e0100
Author: Andreas Tille <tille at 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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