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|
# Copyright (C) 2014 Ion Torrent Systems, Inc. All Rights Reserved
cmake_minimum_required (VERSION 2.6)
project (ion-tvc)
enable_testing()
if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse3")
endif()
message(STATUS "CMAKE_CXX_FLAGS: '${CMAKE_CXX_FLAGS}'")
add_definitions(-DALIGNSTATS_IGNORE)
configure_file (
"${PROJECT_SOURCE_DIR}/IonVersion.cpp.in"
"${PROJECT_BINARY_DIR}/IonVersion.cpp" @ONLY
)
set(ION_VCFLIB_DIR external/vcflib)
set(ION_FREEBAYES_DIR external/freebayes)
include_directories(${ION_VCFLIB_DIR})
include_directories(${ION_FREEBAYES_DIR}/src)
include_directories("/usr/include/jsoncpp")
include_directories("/usr/include/bamtools")
include_directories("${PROJECT_SOURCE_DIR}/VariantCaller")
include_directories("${PROJECT_SOURCE_DIR}/VariantCaller/FlowDistEval")
include_directories("${PROJECT_SOURCE_DIR}/VariantCaller/EnsembleEval")
include_directories("${PROJECT_SOURCE_DIR}/VariantCaller/Bookkeeping")
include_directories("${PROJECT_SOURCE_DIR}/VariantCaller/Reads")
include_directories("${PROJECT_SOURCE_DIR}/VariantCaller/Splice")
include_directories("${PROJECT_SOURCE_DIR}/VariantCaller/Filter")
include_directories("${PROJECT_SOURCE_DIR}/realignment")
include_directories("${PROJECT_SOURCE_DIR}/file-io")
include_directories("${PROJECT_SOURCE_DIR}/BaseCaller")
include_directories("${PROJECT_SOURCE_DIR}/Calibration")
include_directories("${PROJECT_SOURCE_DIR}/Util")
include_directories("${PROJECT_SOURCE_DIR}")
set(tvcSRCS
VariantCaller/VariantCaller.cpp
VariantCaller/BAMWalkerEngine.cpp
VariantCaller/OrderedBAMWriter.cpp
VariantCaller/SampleManager.cpp
VariantCaller/TargetsManager.cpp
VariantCaller/HandleVariant.cpp
VariantCaller/HotspotReader.cpp
VariantCaller/MetricsManager.cpp
VariantCaller/Bookkeeping/MiscUtil.cpp
VariantCaller/Bookkeeping/ExtendParameters.cpp
VariantCaller/Bookkeeping/InputStructures.cpp
VariantCaller/Bookkeeping/VcfFormat.cpp
VariantCaller/Reads/ExtendedReadInfo.cpp
VariantCaller/Splice/ErrorMotifs.cpp
VariantCaller/Splice/LocalContext.cpp
VariantCaller/Splice/ClassifyVariant.cpp
VariantCaller/Splice/ErrorMotifs.cpp
VariantCaller/Splice/SpliceVariantHypotheses.cpp
VariantCaller/Filter/DecisionTreeData.cpp
VariantCaller/Filter/VariantAssist.cpp
VariantCaller/HypothesisEvaluator.cpp
VariantCaller/EnsembleEval/DiagnosticJSON.cpp
VariantCaller/EnsembleEval/BiasGenerator.cpp
VariantCaller/EnsembleEval/SigmaGenerator.cpp
VariantCaller/EnsembleEval/SkewGenerator.cpp
VariantCaller/EnsembleEval/PosteriorInference.cpp
VariantCaller/EnsembleEval/ShortStack.cpp
VariantCaller/EnsembleEval/StackEngine.cpp
VariantCaller/EnsembleEval/CrossHypotheses.cpp
# TODO: Actually build vcflib as a static library and link to variant caller.
# TODO2: Resolve bgzf.c collisions between vcflib and bamtools
${ION_VCFLIB_DIR}/Variant.cpp
${ION_VCFLIB_DIR}/split.cpp
${ION_VCFLIB_DIR}/tabixpp/tabix.cpp
${ION_VCFLIB_DIR}/tabixpp/index.c
${ION_VCFLIB_DIR}/tabixpp/bgzf.c
${ION_FREEBAYES_DIR}/src/AlleleParser.cpp
BaseCaller/PIDloop.cpp
BaseCaller/DPTreephaser.cpp
Calibration/LinearCalibrationModel.cpp
Calibration/FlowAlignment.cpp
Util/OptArgs.cpp
realignment/Realigner.cpp
file-io/ion_util.c
file-io/ion_error.c
${PROJECT_BINARY_DIR}/IonVersion.cpp
)
if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
list(APPEND tvcSRCS
BaseCaller/TreephaserSSE.cpp)
endif()
add_executable(tvc ${tvcSRCS})
target_link_libraries(tvc bamtools z pthread blas lapack armadillo jsoncpp smithwaterman disorder)
add_executable(tvcassembly
VariantCaller/IndelAssembly/IndelAssembly.cpp
VariantCaller/TargetsManager.cpp
VariantCaller/SampleManager.cpp
Util/OptArgs.cpp
Util/Utils.cpp
${PROJECT_BINARY_DIR}/IonVersion.cpp
)
target_link_libraries(tvcassembly bamtools z pthread jsoncpp)
add_executable(tvcutils
VariantCaller/tvcutils/tvcutils.cpp
VariantCaller/tvcutils/prepare_hotspots.cpp
VariantCaller/tvcutils/validate_bed.cpp
VariantCaller/tvcutils/unify_vcf.cpp
VariantCaller/TargetsManager.cpp
Util/OptArgs.cpp
${ION_VCFLIB_DIR}/Variant.cpp
${ION_VCFLIB_DIR}/split.cpp
${ION_VCFLIB_DIR}/tabixpp/tabix.cpp
${ION_VCFLIB_DIR}/tabixpp/index.c
${ION_VCFLIB_DIR}/tabixpp/bgzf.c
${PROJECT_BINARY_DIR}/IonVersion.cpp
)
target_link_libraries(tvcutils bamtools z jsoncpp smithwaterman disorder)
install(TARGETS tvc DESTINATION bin)
install(TARGETS tvcassembly DESTINATION bin)
install(TARGETS tvcutils DESTINATION bin)
install(PROGRAMS bin/variant_caller_pipeline.py DESTINATION bin)
install(DIRECTORY share/TVC/pluginMedia DESTINATION share/TVC)
install(DIRECTORY share/TVC/sse DESTINATION share/TVC)
install(DIRECTORY share/TVC/examples DESTINATION share/TVC)
add_test(NAME tvc_call
COMMAND tvc
)
if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
add_test( tvc_test_1_thread_sse_on
tvc
--input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam
--reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta
--target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed
--error-motifs ${PROJECT_SOURCE_DIR}/share/TVC/sse/motifset.txt
--use-sse-basecaller on
--trim-ampliseq-primers on
--num-threads 1
--output-dir ${PROJECT_BINARY_DIR}/test1
--output-vcf small_variants.vcf
)
endif()
add_test( tvc_test_1_thread_sse_off
tvc
--input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam
--reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta
--target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed
--error-motifs ${PROJECT_SOURCE_DIR}/share/TVC/sse/motifset.txt
--use-sse-basecaller off
--trim-ampliseq-primers on
--num-threads 1
--output-dir ${PROJECT_BINARY_DIR}/test1
--output-vcf small_variants.vcf
)
if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64")
add_test( tvc_test_4_threads_sse_on_with_parameter_file
tvc
--input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam
--reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta
--target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed
--error-motifs ${PROJECT_SOURCE_DIR}/share/TVC/sse/motifset.txt
--parameters-file ${PROJECT_SOURCE_DIR}/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
--use-sse-basecaller on
--trim-ampliseq-primers on
--num-threads 4
--output-dir ${PROJECT_BINARY_DIR}/test2
--output-vcf small_variants.vcf
)
endif()
add_test( tvc_test_4_threads_sse_off_with_parameter_file
tvc
--input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam
--reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta
--target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed
--error-motifs ${PROJECT_SOURCE_DIR}/share/TVC/sse/motifset.txt
--parameters-file ${PROJECT_SOURCE_DIR}/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
--use-sse-basecaller off
--trim-ampliseq-primers on
--num-threads 4
--output-dir ${PROJECT_BINARY_DIR}/test2
--output-vcf small_variants.vcf
)
add_test(tvcutils_call
tvcutils
)
set_tests_properties(tvcutils_call PROPERTIES
PASS_REGULAR_EXPRESSION "Commands"
)
add_test(tvcutils_prepare_hotspots_call
tvcutils prepare_hotspots
)
set_tests_properties(tvcutils_prepare_hotspots_call PROPERTIES
PASS_REGULAR_EXPRESSION "General options"
)
add_test(tvcutils_validate_bed_call
tvcutils validate_bed
)
set_tests_properties(tvcutils_validate_bed_call PROPERTIES
PASS_REGULAR_EXPRESSION "General options"
)
add_test(tvcutils_unify_vcf_call
tvcutils unify_vcf
)
set_tests_properties(tvcutils_unify_vcf_call PROPERTIES
PASS_REGULAR_EXPRESSION "General options"
)
add_test(tvcassembly_call
tvcassembly
)
if(0)
add_test(pipeline
${PROJECT_SOURCE_DIR}/bin/variant_caller_pipeline.py
--input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam
--reference-fasta ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta
--region-bed ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_merged_plain.bed
--primer-trim-bed ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed
--output-dir ${PROJECT_BINARY_DIR}/Testing/variant_caller_pipeline_call
)
add_test(tvc_simple
tvc
--output-dir ${PROJECT_BINARY_DIR}/Testing/tvc_simple
--output-vcf small_variants.vcf
--reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta
--input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam
--target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed
--trim-ampliseq-primers on
--num-threads 12
)
endif()
if (0)
set(test_rm_files)
set(test_file_prefix "AAAA")
set(test_diff_prog "${PROJECT_SOURCE_DIR}/Testing/diffVCF.pl")
set(delta 0.0001)
set(test_name tvc_call2)
set(test_prog "${PROJECT_BINARY_DIR}/tvc")
set(test_cmp_file "${PROJECT_BINARY_DIR}/Testing/${test_name}/small_variants.vcf")
set(test_std_file "${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/expected/small_variants.vcf")
set(test_args
--output-dir ${PROJECT_BINARY_DIR}/Testing/${test_name}
--output-vcf small_variants.vcf
--reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta
--input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam
--target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed
--trim-ampliseq-primers on
--num-threads 12)
add_test(NAME ${test_name} COMMAND ${CMAKE_COMMAND} -V -VV
"-Dtest_name:STRING=${test_name}"
"-Dtest_prog:STRING=${test_prog}"
"-Dtest_prog_args:STRING=${test_args}"
"-Dfile_cmp:FILEPATH=${test_cmp_file}"
"-Dfile_std:FILEPATH=${test_std_file}"
"-Drm_files:STRING=${test_rm_files}"
"-Ddiff_prog:FILEPATH=${test_diff_prog}"
"-Ddelta:FILEPATH=${delta}"
-P "${PROJECT_SOURCE_DIR}/Testing/RunDiffRemoveTest.cmake"
)
set(test_name variant_caller_pipeline_call)
set(test_prog variant_caller_pipeline.py)
set(test_cmp_file "${PROJECT_BINARY_DIR}/Testing/${test_name}/TSVC_variants.vcf")
set(test_std_file "${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/expected/TSVC_variants.vcf")
set(test_args
--input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam
--reference-fasta ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta
--region-bed ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_merged_plain.bed
--primer-trim-bed ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed
--output-dir ${PROJECT_BINARY_DIR}/Testing/variant_caller_pipeline_call)
add_test(NAME ${test_name} COMMAND ${CMAKE_COMMAND} -V -VV
"-Dtest_name:STRING=${test_name}"
"-Dtest_prog:STRING=${test_prog}"
"-Dtest_prog_args:STRING=${test_args}"
"-Dfile_cmp:FILEPATH=${test_cmp_file}"
"-Dfile_std:FILEPATH=${test_std_file}"
"-Drm_files:STRING=${test_rm_files}"
"-Ddiff_prog:FILEPATH=${test_diff_prog}"
"-Ddelta:FILEPATH=${delta}"
-P "${PROJECT_SOURCE_DIR}/Testing/RunDiffRemoveTest.cmake"
)
endif()
if (0)
set(test_name Z06-506-CCP)
set(test_prog variant_caller_pipeline.py)
set(REF /mnt/TS/source/hg19/hg19.fasta)
set(BED_UNMERGED_DETAIL /mnt/TS/source/tvc_test_Z06-506-CCP/unmerged_detail_CCP.20131001.designed.bed)
set(BED_MERGED_PLAIN /mnt/TS/source/tvc_test_Z06-506-CCP/merged_plain_CCP.20131001.designed.bed)
set(BAM /mnt/TS/source/tvc_test_Z06-506-CCP/IonXpress_019_rawlib.bam)
set(TVC_PARAM /mnt/TS/source/tvc_test_Z06-506-CCP/local_parameters.json)
set(HOTSPOT /mnt/TS/source/tvc_test_Z06-506-CCP/hotspot.vcf)
set(test_std_file /mnt/TS/source/tvc_test_Z06-506-CCP/expected/TSVC_variants.vcf)
set(test_cmp_file "${PROJECT_BINARY_DIR}/Testing/${test_name}/TSVC_variants.vcf")
set(TMP_DIR "${PROJECT_BINARY_DIR}/Testing/${test_name}")
set(test_args
--parameters-file ${TVC_PARAM}
--input-bam ${BAM}
--reference-fasta ${REF}
--region-bed ${BED_MERGED_PLAIN}
--primer-trim-bed ${BED_UNMERGED_DETAIL}
--hotspot-vcf ${HOTSPOT}
--postprocessed-bam ${TMP_DIR}/trimmed.bam
--output-dir ${TMP_DIR})
add_test(NAME ${test_name} COMMAND ${CMAKE_COMMAND} -V -VV
"-Dtest_name:STRING=${test_name}"
"-Dtest_prog:STRING=${test_prog}"
"-Dtest_prog_args:STRING=${test_args}"
"-Dfile_cmp:FILEPATH=${test_cmp_file}"
"-Dfile_std:FILEPATH=${test_std_file}"
"-Drm_files:STRING=${test_rm_files}"
"-Ddiff_prog:FILEPATH=${test_diff_prog}"
"-Ddelta:FILEPATH=${delta}"
-P "${PROJECT_SOURCE_DIR}/Testing/RunDiffRemoveTest.cmake"
)
endif()
|
