Description: Use Debian packaged libsmithwaterman
Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 12 Dec 2018 23:05:46 -0500 (see #916322)

--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -85,10 +85,6 @@ set(tvcSRCS
   ${ION_VCFLIB_DIR}/tabixpp/tabix.cpp
   ${ION_VCFLIB_DIR}/tabixpp/index.c
   ${ION_VCFLIB_DIR}/tabixpp/bgzf.c
-  ${ION_VCFLIB_DIR}/smithwaterman/LeftAlign.cpp
-  ${ION_VCFLIB_DIR}/smithwaterman/Repeats.cpp
-  ${ION_VCFLIB_DIR}/smithwaterman/IndelAllele.cpp
-  ${ION_VCFLIB_DIR}/smithwaterman/SmithWatermanGotoh.cpp
   ${ION_FREEBAYES_DIR}/src/AlleleParser.cpp
 
   BaseCaller/PIDloop.cpp
@@ -108,7 +104,7 @@ if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL
 endif()
 
 add_executable(tvc ${tvcSRCS})
-target_link_libraries(tvc bamtools z pthread blas lapack armadillo jsoncpp)
+target_link_libraries(tvc bamtools z pthread blas lapack armadillo jsoncpp smithwaterman disorder)
 
 
 add_executable(tvcassembly
@@ -135,14 +131,10 @@ add_executable(tvcutils
   ${ION_VCFLIB_DIR}/tabixpp/tabix.cpp
   ${ION_VCFLIB_DIR}/tabixpp/index.c
   ${ION_VCFLIB_DIR}/tabixpp/bgzf.c
-  ${ION_VCFLIB_DIR}/smithwaterman/LeftAlign.cpp
-  ${ION_VCFLIB_DIR}/smithwaterman/Repeats.cpp
-  ${ION_VCFLIB_DIR}/smithwaterman/IndelAllele.cpp
-  ${ION_VCFLIB_DIR}/smithwaterman/SmithWatermanGotoh.cpp
   ${PROJECT_BINARY_DIR}/IonVersion.cpp
 )
 
-target_link_libraries(tvcutils bamtools z jsoncpp)
+target_link_libraries(tvcutils bamtools z jsoncpp smithwaterman disorder)
 
 install(TARGETS   tvc                                                 DESTINATION bin)
 install(TARGETS   tvcassembly                                         DESTINATION bin)