Author: Nilesh Patra <npatra974@gmail.com>
Description: Patch CMakeLists.txt to use system libs instead of code copies.
Last-Changed: Wednesday - July 17, 2020
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,8 +1,7 @@
 cmake_minimum_required(VERSION 2.8)
 project(ngmlr)
 
-include_directories (../lib/seqan-library-2.2.0/include)
-include_directories (../lib/Complete-Striped-Smith-Waterman-Library/src)
+include_directories (/usr/include/htslib)
 include_directories (../lib)
 include_directories( ${ZLIB_INCLUDE_DIRS} )
 
@@ -40,7 +39,7 @@
 					OutputReadBuffer.cpp	
 					ScoreBuffer.cpp
 					StrippedSW.cpp
-					../lib/Complete-Striped-Smith-Waterman-Library/src/ssw.c
+					/usr/include/ssw.h
 					unix.cpp
 					unix_threads.cpp)										
 					
@@ -50,5 +49,6 @@
  
 TARGET_LINK_LIBRARIES(ngmlr ${ZLIB_LIBRARIES})
 TARGET_LINK_LIBRARIES(ngmlr ${CMAKE_THREAD_LIBS_INIT})
+TARGET_LINK_LIBRARIES(ngmlr ssw)
 
-install (TARGETS ngmlr DESTINATION bin)
\ No newline at end of file
+install (TARGETS ngmlr DESTINATION bin)