From bc12d3e3d6a9d664fd779b1e922e449bdb05cbae Mon Sep 17 00:00:00 2001
From: Jon Matteo Church <jon.church@nanoporetech.com>
Date: Thu, 28 Sep 2023 14:18:52 +0100
Subject: [PATCH 1/3] allow lib and exe to be built at the same time

---
 CMakeLists.txt | 30 ++++++++++++++++++++----------
 README.md      |  1 +
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b243a19a..1d102816 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,7 +3,8 @@ cmake_minimum_required(VERSION 3.10)
 project(minimap2 VERSION 2.24.0 LANGUAGES C)
 enable_testing()
 
-option(ONT_MM2_EXE "Build minimap2 exe" ON)
+option(ONT_MM2_EXE "Build minimap2 exe" OFF)
+option(ONT_MM2_LIB "Build minimap2 lib" ON)
 
 # set default build type to release
 if (NOT EXISTS ${CMAKE_BINARY_DIR}/CMakeCache.txt)
@@ -75,22 +76,31 @@ set(MM2_SOURCES
 )
 
 if(ONT_MM2_EXE)
-  add_executable(minimap2 ${MM2_SOURCES} src/3rdparty/minimap2/main.c)
-  get_target_property(MM2_BIN_DIR minimap2 SOURCE_DIR)
+  add_executable(minimap2-exe ${MM2_SOURCES} src/3rdparty/minimap2/main.c)
+  list(APPEND TARGETS minimap2-exe)
+  set_target_properties(minimap2-exe PROPERTIES OUTPUT_NAME minimap2)
+  get_target_property(MM2_BIN_DIR minimap2-exe SOURCE_DIR)
   add_test(
     NAME minimap2_version_test
     WORKING_DIRECTORY ${MM2_BIN_DIR}
     COMMAND minimap2 -V
   )
-else()
+endif()
+if(ONT_MM2_LIB)
   add_library(minimap2 ${MM2_SOURCES})
+  list(APPEND TARGETS minimap2)
 endif()
 
 include_directories(${CMAKE_SOURCE_DIR}/src/3rdparty/minimap2) 
-target_link_libraries(minimap2 ${ZLIB_LIBRARIES})
 
-if(NOT WIN32)
-  target_link_libraries(minimap2 m Threads::Threads)
-else()
-  target_link_libraries(minimap2 pthreadVC3)
-endif()
+foreach(TARGET IN LISTS TARGETS)
+  target_link_libraries(${TARGET} ${ZLIB_LIBRARIES})
+
+  if(NOT WIN32)
+    target_link_libraries(${TARGET} m Threads::Threads)
+  else()
+    target_link_libraries(${TARGET} pthreadVC3)
+  endif()
+endforeach()
+
+install(TARGETS ${TARGETS})
diff --git a/README.md b/README.md
index 6c81a736..a893853e 100644
--- a/README.md
+++ b/README.md
@@ -16,3 +16,4 @@ $ ctest -C Release --test-dir cmake-build --output-on-failure
 | CMake                    | Description                                     | Default |
 |:-------------------------|:------------------------------------------------|---------|
 | ONT_MM2_EXE              | Build the minimap2 executable                   | ON      |
+| ONT_MM2_LIB              | Build the minimap2 library                      | OFF     |

From d3115b18bb91bebe3adfbdf9cf5143270c75b2af Mon Sep 17 00:00:00 2001
From: Jon Matteo Church <jon.church@nanoporetech.com>
Date: Thu, 28 Sep 2023 17:21:25 +0100
Subject: [PATCH 2/3] add verbose messages

---
 CMakeLists.txt | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1d102816..1d24266f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -76,18 +76,21 @@ set(MM2_SOURCES
 )
 
 if(ONT_MM2_EXE)
-  add_executable(minimap2-exe ${MM2_SOURCES} src/3rdparty/minimap2/main.c)
-  list(APPEND TARGETS minimap2-exe)
-  set_target_properties(minimap2-exe PROPERTIES OUTPUT_NAME minimap2)
-  get_target_property(MM2_BIN_DIR minimap2-exe SOURCE_DIR)
+  add_executable(minimap2_exe ${MM2_SOURCES} src/3rdparty/minimap2/main.c)
+  message(STATUS "added exec: minimap2_exe")
+  list(APPEND TARGETS minimap2_exe)
+  set_target_properties(minimap2_exe PROPERTIES OUTPUT_NAME minimap2)
+  get_target_property(MM2_BIN_DIR minimap2_exe SOURCE_DIR)
   add_test(
     NAME minimap2_version_test
     WORKING_DIRECTORY ${MM2_BIN_DIR}
     COMMAND minimap2 -V
   )
+  message(STATUS "added test: minimap2_version_test")
 endif()
 if(ONT_MM2_LIB)
   add_library(minimap2 ${MM2_SOURCES})
+  message(STATUS "added lib: minimap2")
   list(APPEND TARGETS minimap2)
 endif()
 

From 57bddc46260e1b13092c5d873a73987c85d39c00 Mon Sep 17 00:00:00 2001
From: Jon Matteo Church <jon.church@nanoporetech.com>
Date: Fri, 29 Sep 2023 09:40:41 +0100
Subject: [PATCH 3/3] fix minimap2_version_test

---
 CMakeLists.txt | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1d24266f..2952871f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -77,20 +77,15 @@ set(MM2_SOURCES
 
 if(ONT_MM2_EXE)
   add_executable(minimap2_exe ${MM2_SOURCES} src/3rdparty/minimap2/main.c)
-  message(STATUS "added exec: minimap2_exe")
   list(APPEND TARGETS minimap2_exe)
   set_target_properties(minimap2_exe PROPERTIES OUTPUT_NAME minimap2)
-  get_target_property(MM2_BIN_DIR minimap2_exe SOURCE_DIR)
   add_test(
     NAME minimap2_version_test
-    WORKING_DIRECTORY ${MM2_BIN_DIR}
-    COMMAND minimap2 -V
+    COMMAND minimap2_exe -V
   )
-  message(STATUS "added test: minimap2_version_test")
 endif()
 if(ONT_MM2_LIB)
   add_library(minimap2 ${MM2_SOURCES})
-  message(STATUS "added lib: minimap2")
   list(APPEND TARGETS minimap2)
 endif()