From b9a643f3e361abd1aa9cd112e76d766014c0ef9d Mon Sep 17 00:00:00 2001
From: Bryce Lorenz Kille <brycekille@gmail.com>
Date: Tue, 22 Aug 2023 11:52:45 -0500
Subject: [PATCH] Use PkgConfig, as suggested in #61

---
 CMakeLists.txt | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8c1f91a..ff08dc1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -26,6 +26,8 @@ endif()
 option(USE_HTSLIB "Compile with htslib for --targetPrefix and --targetList" OFF)
 if (USE_HTSLIB)
   add_definitions(-DUSE_HTSLIB)
+  find_package(PkgConfig)
+  pkg_check_modules(HTSLIB REQUIRED IMPORTED_TARGET htslib)
 endif()
 option(PROFILE             "Prevent inlining and add debug symbols" OFF)
 
@@ -73,13 +75,17 @@ add_executable(mashmap-align
 target_include_directories(mashmap PRIVATE
   src
   src/common
-  )
+)
 
 target_include_directories(mashmap-align PRIVATE
   src
   src/common
-  )
+)
 
+if (USE_HTSLIB)
+  target_link_libraries(mashmap PkgConfig::HTSLIB)
+  target_link_libraries(mashmap-align PkgConfig::HTSLIB)
+endif()
 
 target_link_libraries(mashmap
   gsl
@@ -90,9 +96,6 @@ target_link_libraries(mashmap
   z
   #assert
 )
-if (USE_HTSLIB)
-  target_link_libraries(mashmap hts)
-endif()
 
 target_link_libraries(mashmap-align
   gsl
@@ -103,9 +106,6 @@ target_link_libraries(mashmap-align
   z
   #assert
 )
-if (USE_HTSLIB)
-  target_link_libraries(mashmap-align hts)
-endif()
 
 install(TARGETS mashmap DESTINATION bin)
 install(TARGETS mashmap-align DESTINATION bin)