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diff --git a/CMakeLists.txt b/CMakeLists.txt
index af3fe67..f237563 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -63,8 +63,10 @@ set_package_properties(ZLIB PROPERTIES TYPE REQUIRED)
find_package(Threads)
set_package_properties(Threads PROPERTIES TYPE REQUIRED)
-pkg_check_modules(htslib IMPORTED_TARGET htslib) # Optionally builds from contrib/
-pkg_check_modules(tabixpp IMPORTED_TARGET tabixpp) # Optionally builds from contrib/
+pkg_check_modules(htslib IMPORTED_TARGET htslib) # Optionally builds from contrib/
+pkg_check_modules(tabixpp IMPORTED_TARGET tabixpp) # Optionally builds from contrib/
+pkg_check_modules(fastahack IMPORTED_TARGET fastahack) # Optionally builds from contrib/
+pkg_check_modules(smithwaterman IMPORTED_TARGET smithwaterman) # Optionally builds from contrib/
# ---- Build switches
set(CMAKE_INTERPROCEDURAL_OPTIMIZATION ${ipo_supported})
@@ -113,12 +115,20 @@ endif(ZIG)
# ---- Include files
include_directories(include)
-include_directories(contrib/fastahack)
include_directories(contrib/intervaltree)
-include_directories(contrib/smithwaterman)
include_directories(contrib/filevercmp)
include_directories(contrib/c-progress-bar)
+if(NOT fastahack_FOUND)
+ message(STATUS "Using included fastahack")
+ include_directories(contrib/fastahack)
+endif()
+
+if(NOT smithwaterman_FOUND)
+ message(STATUS "Using included smithwaterman")
+ include_directories(contrib/smithwaterman)
+endif()
+
if(NOT htslib_FOUND)
message(STATUS "Using included htslib")
include(FindCURL) # for htslib
@@ -142,11 +152,19 @@ endif()
file(GLOB INCLUDES
src/*.h*
contrib/intervaltree/*.h*
- contrib/smithwaterman/*.h*
- contrib/fastahack/*.h*
contrib/filevercmp/*.h*
)
+if(NOT fastahack_FOUND)
+ file(GLOB FASTAHACK_INCLUDES contrib/fastahack/*.h*)
+ list(APPEND INCLUDES ${FASTAHACK_INCLUDES})
+endif()
+
+if(NOT smithwaterman_FOUND)
+ file(GLOB SW_INCLUDES contrib/smithwaterman/*.h*)
+ list(APPEND INCLUDES ${SW_INCLUDES})
+endif()
+
set(vcfwfa_SOURCE
src/legacy.cpp # introduces a WFA dependency
src/vcf-wfa.cpp
@@ -170,16 +188,24 @@ set(vcflib_SOURCE
src/LeftAlign.cpp
src/cigar.cpp
src/allele.cpp
- contrib/fastahack/Fasta.cpp
+ contrib/fsom/fsom.c
+ contrib/filevercmp/filevercmp.c
+ contrib/c-progress-bar/progress.c
+)
+
+if(NOT fastahack_FOUND)
+ list(APPEND vcflib_SOURCE contrib/fastahack/Fasta.cpp)
+endif()
+
+if(NOT smithwaterman_FOUND)
+ list(APPEND vcflib_SOURCE
contrib/smithwaterman/SmithWatermanGotoh.cpp
contrib/smithwaterman/Repeats.cpp
contrib/smithwaterman/IndelAllele.cpp
contrib/smithwaterman/disorder.cpp
contrib/smithwaterman/LeftAlign.cpp
- contrib/fsom/fsom.c
- contrib/filevercmp/filevercmp.c
- contrib/c-progress-bar/progress.c
-)
+ )
+endif()
if (tabixpp_LOCAL) # add the tabixpp source file
list(APPEND vcflib_SOURCE ${tabixpp_SOURCE})
@@ -440,6 +466,14 @@ if (NOT tabixpp_LOCAL)
target_link_libraries(vcflib PkgConfig::tabixpp)
endif()
+if(fastahack_FOUND)
+ target_link_libraries(vcflib PkgConfig::fastahack)
+endif()
+
+if(smithwaterman_FOUND)
+ target_link_libraries(vcflib PkgConfig::smithwaterman)
+endif()
+
if(OPENMP)
target_link_libraries(vcflib OpenMP::OpenMP_CXX)
endif()
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