Author: Michael R. Crusoe <mcrusoe@msu.edu>
Last-Update: Thu, 12 Feb 2015 09:21:09 +0100
Description: Fix path to Debian packaged bamtools

--- express.orig/CMakeLists.txt
+++ express/CMakeLists.txt
@@ -33,10 +33,11 @@
 
 find_package(Protobuf)
 if (PROTOBUF_FOUND)
-  include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") 
+  include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR}
+	  "/usr/include/bamtools") 
 	set(PROTO_INT 1)
 else (PROTOBUF_FOUND)
-  include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") 
+  include_directories(${Boost_INCLUDE_DIRS} "/usr/include/bamtools") 
 	set(PROTO_INT 0)
 endif(PROTOBUF_FOUND)
 
--- express.orig/src/CMakeLists.txt
+++ express/src/CMakeLists.txt
@@ -16,7 +16,7 @@
 if(WIN32)
   set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib")
 else(WIN32)
-  set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread")
+  set(LIBRARIES ${LIBRARIES} "libbamtools.so" "pthread")
 endif(WIN32)
 
 if (PROTOBUF_FOUND)
--- express.orig/src/mismatchmodel.cpp
+++ express/src/mismatchmodel.cpp
@@ -126,7 +126,7 @@
   size_t k = 0;
   do {
     if (k > max_indel_size) {
-      logger.warn("Paramater file '%s' insertion distribution is being "
+      logger.warn("Parameter file '%s' insertion distribution is being "
                   "truncated at max indel length of %d.",
                   param_file_name.c_str(), max_indel_size);
       break;
@@ -143,7 +143,7 @@
   k = 0;
   do {
     if (k > max_indel_size) {
-      logger.warn("Paramater file '%s' deletion distribution is being "
+      logger.warn("Parameter file '%s' deletion distribution is being "
                   "truncated at max indel length of %d.",
                   param_file_name.c_str(), max_indel_size);
       break;
