Author: Andreas Tille <tille@debian.org>
Last-Update: 2021-01-28
Description: Use Debian packaged libsmithwaterman
Forwarded: not-needed
--- libvcflib.orig/CMakeLists.txt
+++ libvcflib/CMakeLists.txt
@@ -59,6 +59,7 @@
 
 pkg_check_modules(HTSLIB htslib)   # Optionally builds from contrib/
 pkg_check_modules(TABIXPP tabixpp) # Optionally builds from contrib/
+pkg_check_modules(SMITHWATERMAN REQUIRED IMPORTED_TARGET libsmithwaterman)
 
 # ---- Build switches
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -110,7 +111,6 @@
 include_directories(include)
 include_directories(contrib/fastahack)
 include_directories(contrib/intervaltree)
-include_directories(contrib/smithwaterman)
 # include_directories(contrib/multichoose) merged with vcflib
 include_directories(contrib/filevercmp)
 include_directories(contrib/c-progress-bar)
@@ -146,7 +146,6 @@
   src/*.h*
   # contrib/multichoose/*.h*
   contrib/intervaltree/*.h*
-  contrib/smithwaterman/*.h*
   contrib/fastahack/*.h*
   contrib/filevercmp/*.h*
   )
@@ -172,15 +171,14 @@
     src/cigar.cpp
     src/allele.cpp
     contrib/fastahack/Fasta.cpp
-    contrib/smithwaterman/SmithWatermanGotoh.cpp
-    contrib/smithwaterman/Repeats.cpp
-    contrib/smithwaterman/IndelAllele.cpp
-    contrib/smithwaterman/disorder.cpp
-    contrib/smithwaterman/LeftAlign.cpp
     contrib/filevercmp/filevercmp.c
     contrib/c-progress-bar/progress.c
 )
 
+target_link_libraries(vcflib
+    PkgConfig::SMITHWATERMAN
+    )
+
 if (TABIXPP_LOCAL) # add the tabixpp source file
     list(APPEND vcflib_SOURCE ${tabixpp_SOURCE})
 endif()