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

--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -33,10 +33,11 @@ endif(GPERFTOOLS_TCMALLOC_LIB)
 
 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)
 
@@ -52,7 +53,9 @@ else(WIN32)
     if (EXISTS "${PROJECT_SOURCE_DIR}/bamtools/lib/libbamtools.a")
       set(BAMTOOLS_LIBRARIES "${PROJECT_SOURCE_DIR}/bamtools/lib/libbamtools.a")
     else()
-      find_library(BAMTOOLS_LIBRARIES libbamtools.a)
+      # find_library(BAMTOOLS_LIBRARIES libbamtools.a)
+      message(STATUS "Do not try to find libbamtools.a")
+      set(BAMTOOLS_LIBRARIES bamtools)
     endif()
 	find_package(ZLIB REQUIRED)
 	set(WIN32_INT 0)
--- a/src/mismatchmodel.cpp
+++ b/src/mismatchmodel.cpp
@@ -126,7 +126,7 @@ MismatchTable::MismatchTable(string para
   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 @@ MismatchTable::MismatchTable(string para
   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;
