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Author: Michael R. Crusoe <mcrusoe@msu.edu>
Last-Update: Thu, 12 Feb 2015 09:21:09 +0100
Description: Fix path to Debian packaged bamtools
--- berkeley-express.orig/CMakeLists.txt
+++ berkeley-express/CMakeLists.txt
@@ -36,10 +36,11 @@
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)
@@ -55,7 +56,9 @@
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)
--- berkeley-express.orig/src/mismatchmodel.cpp
+++ berkeley-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;
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