Add pthreads back into CMake for htslib linking

CMakeLists.txt

@@ -367,6 +367,8 @@ if(GENESIS_USE_HTSLIB)
     SET( GENESIS_HTSLIB_VERSION "1.16" ) #GENESIS_HTSLIB_VERSION#
 
     # Included from modules dir tools/cmake
+    # htslib needs pthreads to be linked, so we include this here as well
+    include( IncludePthreads )
     include( IncludeHtslib )
 
 endif()
@@ -468,6 +470,9 @@ IF( GENESIS_HAS_PARENT_DIR )
     if(ZLIB_FOUND)
         set( ZLIB_FOUND ${ZLIB_FOUND} PARENT_SCOPE )
     endif()
+    if(THREADS_FOUND)
+        set( THREADS_FOUND ${THREADS_FOUND} PARENT_SCOPE )
+    endif()
     if(OPENMP_FOUND)
         set( OPENMP_FOUND ${OPENMP_FOUND} PARENT_SCOPE )
     endif()

tools/cmake/IncludePthreads.cmake

@@ -23,10 +23,11 @@
 #   Use PThreads
 # ------------------------------------------------------------------------------
 
-# This file can be included from the main CMakeLists.txt in order to figure out
+# This file is included from the main CMakeLists.txt in order to figure out
 # if Pthreads are available, and if so, set its paths and flags.
-# We curently do not use this any more, as we have switched to just using
-# the plain C++11 threading model instead. We keep this here for reference only.
+# We curently do not use pthreads internally any more, as we have switched to just using
+# the plain C++11 threading model instead. However, they seem to be needed for properly
+# linking htslib... So we have to keep this around.
 
 message (STATUS "Looking for Threads")
 set (CMAKE_THREAD_PREFER_PTHREAD ON)