<commit_before># ===========================================================================
#                  SeqAn - The Library for Sequence Analysis
# ===========================================================================
# File: /apps/pair_align/CMakeLists.txt
#
# CMakeLists.txt file for pair_align.
# ===========================================================================

cmake_minimum_required (VERSION 2.8.2)
project (seqan_apps_pair_align)
message (STATUS "Configuring apps/pair_align")

set (SEQAN_APP_VERSION "1.2")

# ----------------------------------------------------------------------------
# Dependencies
# ----------------------------------------------------------------------------

# Search SeqAn and select dependencies.
set (SEQAN_FIND_DEPENDENCIES NONE)
find_package (SeqAn REQUIRED)

# ----------------------------------------------------------------------------
# Build Setup
# ----------------------------------------------------------------------------

# Add include directories.
include_directories (${SEQAN_INCLUDE_DIRS})

# Add definitions set by find_package (SeqAn).
add_definitions (${SEQAN_DEFINITIONS})

# Add definitions set by the build system.
add_definitions (-DSEQAN_APP_VERSION="${SEQAN_APP_VERSION}")
add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}")
add_definitions (-DSEQAN_DATE="${SEQAN_DATE}")

# Update the list of file names below if you add source files to your application.
add_executable (pair_align pair_align.cpp)

#Before linking create static library for pair_align
# Include lib folder to build the static library pair_align_lib.
add_subdirectory(lib)

# Add dependencies found by find_package (SeqAn).
target_link_libraries (pair_align pair_align_lib ${SEQAN_LIBRARIES})

# Add CXX flags found by find_package (SeqAn).
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")

# ----------------------------------------------------------------------------
# Installation
# ----------------------------------------------------------------------------

# Set variables for installing, depending on the selected build type.<commit_msg>[FIX] move the deifinition of CMAKE_CXX_FLAGS before add_subdirectory(lib) is invoked. Otherwise the CMAKE_CXX_FLAGS are not defined (W2 flag missing) in the subdirectory. I dont know if this behaviour is a bug or feature of cmake.<commit_after># ===========================================================================
#                  SeqAn - The Library for Sequence Analysis
# ===========================================================================
# File: /apps/pair_align/CMakeLists.txt
#
# CMakeLists.txt file for pair_align.
# ===========================================================================

cmake_minimum_required (VERSION 2.8.2)
project (seqan_apps_pair_align)
message (STATUS "Configuring apps/pair_align")

set (SEQAN_APP_VERSION "1.2")

# ----------------------------------------------------------------------------
# Dependencies
# ----------------------------------------------------------------------------

# Search SeqAn and select dependencies.
set (SEQAN_FIND_DEPENDENCIES NONE)
find_package (SeqAn REQUIRED)

# ----------------------------------------------------------------------------
# Build Setup
# ----------------------------------------------------------------------------

# Add include directories.
include_directories (${SEQAN_INCLUDE_DIRS})

# Add definitions set by find_package (SeqAn).
add_definitions (${SEQAN_DEFINITIONS})

# Add definitions set by the build system.
add_definitions (-DSEQAN_APP_VERSION="${SEQAN_APP_VERSION}")
add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}")
add_definitions (-DSEQAN_DATE="${SEQAN_DATE}")

# Add CXX flags found by find_package (SeqAn).
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")

# Update the list of file names below if you add source files to your application.
add_executable (pair_align pair_align.cpp)

#Before linking create static library for pair_align
# Include lib folder to build the static library pair_align_lib.
add_subdirectory(lib)

# Add dependencies found by find_package (SeqAn).
target_link_libraries (pair_align pair_align_lib ${SEQAN_LIBRARIES})

# ----------------------------------------------------------------------------
# Installation
# ----------------------------------------------------------------------------

# Set variables for installing, depending on the selected build type.
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