Author: Michael R. Crusoe <crusoe@ucdavis.edu>
Description: Use system copy of bamtools
--- transrate-tools.orig/CMakeLists.txt
+++ transrate-tools/CMakeLists.txt
@@ -19,11 +19,13 @@
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
 
-SET(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS)
+#SET(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS)
 
 ## Set the standard required compile flags
 set (CMAKE_CXX_FLAGS "-fPIC -O3 -DHAVE_ANSI_TERM -DHAVE_SSTREAM -DHAVE_CONFIG_H -Wall -std=c++11")
-set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+#set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+
+find_package(bamtools REQUIRED)
 
 ##
 # Record this top-level path
@@ -33,14 +35,14 @@
 # Have CMake tell us what it's doing
 set (CMAKE_VERBOSE_MAKEFILE true)
 
-if("${CMAKE_SYSTEM}" MATCHES "Linux")
-  set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
-endif("${CMAKE_SYSTEM}" MATCHES "Linux")
+#if("${CMAKE_SYSTEM}" MATCHES "Linux")
+#  set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+#endif("${CMAKE_SYSTEM}" MATCHES "Linux")
 
 if(APPLE)
   find_package (ZLIB REQUIRED)
 else()
-  find_package (ZLIB REQUIRED STATIC)
+  find_package (ZLIB REQUIRED)
 endif()
 
 # Recurse into transrate-tools source directory
--- transrate-tools.orig/src/CMakeLists.txt
+++ transrate-tools/src/CMakeLists.txt
@@ -2,13 +2,9 @@
 set(BAMREAD_HEADERS pileup.h segmenter.h)
 
 
-include_directories(${GAT_SOURCE_DIR}/bamtools/include)
-link_directories(${GAT_SOURCE_DIR}/bamtools/lib)
-
-set(LIBRARIES ${GAT_SOURCE_DIR}/bamtools/lib/libbamtools.a ${ZLIB_LIBRARIES})
+include_directories(${bamtools_INCLUDE_DIRS})
 
+set(LIBRARIES ${bamtools_LIBRARY})
 add_executable(bam-read ${BAMREAD_SRCS} ${BAMREAD_HEADERS})
 
-set_target_properties(bam-read PROPERTIES LINK_SEARCH_START_STATIC 1)
-set_target_properties(bam-read PROPERTIES LINK_SEARCH_END_STATIC 1)
 target_link_libraries(bam-read ${LIBRARIES})
--- transrate-tools.orig/src/bam-read.h
+++ transrate-tools/src/bam-read.h
@@ -3,7 +3,7 @@
 #include <iostream>
 #include <fstream>
 #include <vector>
-#include "api/BamReader.h"
+#include "/usr/include/bamtools/api/BamReader.h"
 #include "pileup.h"
 
 using namespace BamTools;
--- transrate-tools.orig/src/pileup.h
+++ transrate-tools/src/pileup.h
@@ -2,7 +2,7 @@
 #include <string>
 #include <vector>
 #include <math.h>
-#include "api/BamAlignment.h"
+#include "/usr/include/bamtools/api/BamAlignment.h"
 #include "segmenter.h"
 
 extern double nullprior;
