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# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
if ( Java_FOUND )
include(UseJava)
set( SOURCES
AlignTest.java
AlignSliceTest.java
FragTest.java
PileupTest.java
RefTest.java
ReadGroupTest.java
DumpReferenceFASTA.java
)
add_jar( ngs-examples
SOURCES ${SOURCES}
INCLUDE_JARS ngs-java
OUTPUT_DIR ${CMAKE_JAR_OUTPUT_DIRECTORY}
)
if ( SINGLE_CONFIG )
if ( NOT TOOLS_ONLY )
# LOGLEVEL values: WARNING (default), OFF, INFO, FINE, FINER, FINEST
set( LOGLEVEL OFF )
macro( RunAndDiff TestName TestParams )
add_test(
NAME Test_NgsJavaExamples_${TestName}
COMMAND
${CMAKE_COMMAND} -E env NCBI_SETTINGS=/
${CMAKE_COMMAND} -E env NCBI_VDB_QUALITY=R
sh -c
"\"${Java_JAVA_EXECUTABLE}\" -Dvdb.log=${LOGLEVEL} -cp ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-examples.jar:${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-java.jar -Djava.library.path=${CMAKE_LIBRARY_OUTPUT_DIRECTORY} examples.${TestName} ${TestParams} > ${CMAKE_CURRENT_SOURCE_DIR}/actual/${TestName} && diff ${CMAKE_CURRENT_SOURCE_DIR}/expected/${TestName} ${CMAKE_CURRENT_SOURCE_DIR}/actual/${TestName}"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
COMMAND_EXPAND_LISTS
)
set_tests_properties(Test_NgsJavaExamples_${TestName}
PROPERTIES LABELS "online")
endmacro()
RunAndDiff( FragTest "ERR225922 10000 2" )
RunAndDiff( AlignTest "ERR225922 10000 2" )
RunAndDiff( AlignSliceTest "SRR1121656 1 1 9999" )
RunAndDiff( PileupTest "SRR1121656 1 9999 10003" )
RunAndDiff( RefTest "SRR1121656" )
RunAndDiff( ReadGroupTest "SRR1121656" )
RunAndDiff( DumpReferenceFASTA "SRR520124 1" )
endif()
set( INSTALL_DEST ${CMAKE_INSTALL_PREFIX}/share/examples-java )
install(FILES ${SOURCES}
DESTINATION ${INSTALL_DEST}/examples )
install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/Makefile.install
DESTINATION ${INSTALL_DEST}
RENAME Makefile
)
install(FILES README.install
DESTINATION ${INSTALL_DEST}
RENAME README.txt
)
install(FILES expected.txt
DESTINATION ${INSTALL_DEST} )
endif()
install( FILES ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-examples.jar DESTINATION ${CMAKE_INSTALL_PREFIX}/jar/ )
endif()
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