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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required(VERSION 2.8.4)
project(cramore)
set(CMAKE_CXX_STANDARD 14)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-result -O3")
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin")
find_path(HTS_INCLUDE_DIRS htslib/bgzf.h HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT HTS_INCLUDE_DIRS )
message(FATAL_ERROR "libhts HTS_INCLUDE_DIRS not found")
endif()
message(STATUS ${HTS_INCLUDE_DIRS})
#set(CMAKE_FIND_LIBRARY_SUFFIXES ".a;${CMAKE_FIND_LIBRARY_SUFFIXES}")
find_library(HTS_LIBRARIES hts HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT HTS_LIBRARIES)
message(FATAL_ERROR "libhts HTS_LIBRARIES not found")
endif()
message(STATUS ${HTS_LIBRARIES})
set(CMAKE_INCLUDE_CURRENT_DIR ON)
#include_directories(${CMAKE_BINARY_DIR} ${HTS_INCLUDE_DIRS})
include_directories(${HTS_INCLUDE_DIRS})
add_executable(cramore
allele.cpp
allele.h
ancestry_estimator.cpp
ancestry_estimator.h
augmented_bam_record.cpp
augmented_bam_record.h
bam_ordered_reader.cpp
bam_ordered_reader.h
bam_pool.h
bcf_chunked_reader.cpp
bcf_chunked_reader.h
bcf_filter_arg.h
bcf_filtered_reader.cpp
bcf_filtered_reader.h
bcf_ordered_reader.cpp
bcf_ordered_reader.h
bcf_ordered_writer.cpp
bcf_ordered_writer.h
bcf_variant_key.h
boolParser.h
bgzf.h
cmd_bed_delta_svm_train.cpp
cmd_bed_matched_shuffle.cpp
cmd_bed_shuffle.cpp
cmd_bgen_to_vcf.cpp
cmd_cram_context_indel_analysis.cpp
cmd_cram_demuxlet.cpp
cmd_cram_dense_genotype.cpp
cmd_cram_digital_pileup.cpp
cmd_cram_dsc_dump.cpp
cmd_cram_dsc_dump2pileup.cpp
cmd_cram_dsc_pileup.cpp
cmd_cram_flagstat.cpp
cmd_cram_freemux2.cpp
cmd_cram_freemuxlet.cpp
cmd_cram_gtf_util.cpp
cmd_cram_mux_pileup.cpp
cmd_cram_procap_detect.cpp
cmd_cram_simul_contam.cpp
cmd_cram_simuxlet.cpp
cmd_cram_sparse_genotype.cpp
cmd_cram_update_rg.cpp
cmd_cram_verify_bam.cpp
cmd_cram_verify_pair_id.cpp
cmd_dge_barcode_summary.cpp
cmd_dge_shuffle.cpp
cmd_fasta_gc_content.cpp
cmd_plp_find_mux_clust.cpp
cmd_plp_make_dge_matrix.cpp
cmd_sc_kallisto_count.cpp
cmd_sc_map_stamps.cpp
cmd_sc_multinom_em.cpp
cmd_sc_multinom_gibbs.cpp
cmd_tsv_util.cpp
cmd_vcf_delta_svm.cpp
cmd_vcf_extract.cpp
cmd_vcf_fill_plink2.cpp
cmd_vcf_ibs_matrix.cpp
cmd_vcf_ibs0_summary.cpp
cmd_vcf_ibs0_phase.cpp
cmd_vcf_ref_phase.cpp
cmd_vcf_infer_ancestry.cpp
cmd_vcf_infer_isaf.cpp
cmd_vcf_mendel_dup_conc.cpp
cmd_vcf_merge_candidate_variants.cpp
cmd_vcf_normalize_depth.cpp
cmd_vcf_paste_calls.cpp
cmd_vcf_sample_summary.cpp
cmd_vcf_squeeze.cpp
cmd_vcf_svd.cpp
cmd_vcf_update_info.cpp
cmd_vcf_update_sites.cpp
cmd_run_test.cpp
commands.cpp
commands.h
compact_matrix.cpp
compact_matrix.h
Constant.h
contam_estimator.cpp
contam_estimator.h
cramore.cpp
cramore.h
discrete_log_helper.h
dropseq.cpp
dropseq.h
dsc_dge.cpp
dsc_dge.h
dsc_lib.h
Error.cpp
Error.h
emPhaser.h
emPhaser.cpp
m3vcf.h
m3vcf.cpp
cmd_m3vcf_subsample.cpp
estimator.cpp
estimator.h
fastaGC.cpp
fastaGC.h
filter.cpp
filter.h
bcftools.h
frequency_estimator.cpp
frequency_estimator.h
fVcf.h
genomeChunk.cpp
genomeChunk.h
genome_interval.cpp
genome_interval.h
genomeLoci.h
genotype_concordance.cpp
genotype_concordance.h
gtf.cpp
gtf.h
gtf_interval_tree.h
hFile.h
hts_utils.cpp
hts_utils.h
interval.cpp
interval.h
interval_tree.cpp
interval_tree.h
inVcfArg.h
IO.cpp
IO.h
joint_genotype_block_reader.cpp
joint_genotype_block_reader.h
joint_genotype_block_record.cpp
joint_genotype_block_record.h
libsvm.cpp
libsvm_gkm.cpp
libsvm_gkm.h
libsvm.h
log_tool.cpp
log_tool.h
louvain.h
MathConstant.h
MathGenMin.cpp
MathGenMin.h
MathGold.cpp
MathGold.h
MathMatrix.cpp
MathMatrix.h
MathVector.cpp
MathVector.h
nuclear_pedigree.cpp
nuclear_pedigree.h
params.cpp
params.h
pException.h
pFile.h
PhredHelper.cpp
PhredHelper.h
Random.cpp
Random.h
reference_sequence.cpp
reference_sequence.h
sam_filtered_reader.cpp
sam_filtered_reader.h
sam_ordered_writer.cpp
sam_ordered_writer.h
sc_drop_seq.cpp
sc_drop_seq.h
sex_ploidy_map.cpp
sex_ploidy_map.h
Sort.cpp
Sort.h
tabix.h
tsv_reader.cpp
tsv_reader.h
utils.cpp
utils.h
var_dict.h
variant.cpp
variant.h
variant_manip.cpp
variant_manip.h
vntr.cpp
vntr.h
wFile.h
Eigen/Cholesky
Eigen/CholmodSupport
Eigen/Core
Eigen/Dense
Eigen/Eigen
Eigen/Eigenvalues
Eigen/Geometry
Eigen/Householder
Eigen/IterativeLinearSolvers
Eigen/Jacobi
Eigen/LU
Eigen/MetisSupport
Eigen/OrderingMethods
Eigen/PaStiXSupport
Eigen/PardisoSupport
Eigen/QR
Eigen/QtAlignedMalloc
Eigen/SPQRSupport
Eigen/SVD
Eigen/Sparse
Eigen/SparseCholesky
Eigen/SparseCore
Eigen/SparseLU
Eigen/SparseQR
Eigen/StdDeque
Eigen/StdList
Eigen/StdVector
Eigen/SuperLUSupport
Eigen/UmfPackSupport
Eigen/src/Cholesky/LDLT.h
Eigen/src/Cholesky/LLT.h
Eigen/src/Cholesky/LLT_LAPACKE.h
Eigen/src/CholmodSupport/CholmodSupport.h
Eigen/src/Core/Array.h
Eigen/src/Core/ArrayBase.h
Eigen/src/Core/ArrayWrapper.h
Eigen/src/Core/Assign.h
Eigen/src/Core/AssignEvaluator.h
Eigen/src/Core/Assign_MKL.h
Eigen/src/Core/BandMatrix.h
Eigen/src/Core/Block.h
Eigen/src/Core/BooleanRedux.h
Eigen/src/Core/CommaInitializer.h
Eigen/src/Core/ConditionEstimator.h
Eigen/src/Core/CoreEvaluators.h
Eigen/src/Core/CoreIterators.h
Eigen/src/Core/CwiseBinaryOp.h
Eigen/src/Core/CwiseNullaryOp.h
Eigen/src/Core/CwiseTernaryOp.h
Eigen/src/Core/CwiseUnaryOp.h
Eigen/src/Core/CwiseUnaryView.h
Eigen/src/Core/DenseBase.h
Eigen/src/Core/DenseCoeffsBase.h
Eigen/src/Core/DenseStorage.h
Eigen/src/Core/Diagonal.h
Eigen/src/Core/DiagonalMatrix.h
Eigen/src/Core/DiagonalProduct.h
Eigen/src/Core/Dot.h
Eigen/src/Core/EigenBase.h
Eigen/src/Core/ForceAlignedAccess.h
Eigen/src/Core/Fuzzy.h
Eigen/src/Core/GeneralProduct.h
Eigen/src/Core/GenericPacketMath.h
Eigen/src/Core/GlobalFunctions.h
Eigen/src/Core/IO.h
Eigen/src/Core/Inverse.h
Eigen/src/Core/Map.h
Eigen/src/Core/MapBase.h
Eigen/src/Core/MathFunctions.h
Eigen/src/Core/MathFunctionsImpl.h
Eigen/src/Core/Matrix.h
Eigen/src/Core/MatrixBase.h
Eigen/src/Core/NestByValue.h
Eigen/src/Core/NoAlias.h
Eigen/src/Core/NumTraits.h
Eigen/src/Core/PermutationMatrix.h
Eigen/src/Core/PlainObjectBase.h
Eigen/src/Core/Product.h
Eigen/src/Core/ProductEvaluators.h
Eigen/src/Core/Random.h
Eigen/src/Core/Redux.h
Eigen/src/Core/Ref.h
Eigen/src/Core/Replicate.h
Eigen/src/Core/ReturnByValue.h
Eigen/src/Core/Reverse.h
Eigen/src/Core/Select.h
Eigen/src/Core/SelfAdjointView.h
Eigen/src/Core/SelfCwiseBinaryOp.h
Eigen/src/Core/Solve.h
Eigen/src/Core/SolveTriangular.h
Eigen/src/Core/SolverBase.h
Eigen/src/Core/StableNorm.h
Eigen/src/Core/Stride.h
Eigen/src/Core/Swap.h
Eigen/src/Core/Transpose.h
Eigen/src/Core/Transpositions.h
Eigen/src/Core/TriangularMatrix.h
Eigen/src/Core/VectorBlock.h
Eigen/src/Core/VectorwiseOp.h
Eigen/src/Core/Visitor.h
Eigen/src/Core/arch/AVX/Complex.h
Eigen/src/Core/arch/AVX/MathFunctions.h
Eigen/src/Core/arch/AVX/PacketMath.h
Eigen/src/Core/arch/AVX/TypeCasting.h
Eigen/src/Core/arch/AVX512/MathFunctions.h
Eigen/src/Core/arch/AVX512/PacketMath.h
Eigen/src/Core/arch/AltiVec/Complex.h
Eigen/src/Core/arch/AltiVec/MathFunctions.h
Eigen/src/Core/arch/AltiVec/PacketMath.h
Eigen/src/Core/arch/CUDA/Complex.h
Eigen/src/Core/arch/CUDA/Half.h
Eigen/src/Core/arch/CUDA/MathFunctions.h
Eigen/src/Core/arch/CUDA/PacketMath.h
Eigen/src/Core/arch/CUDA/PacketMathHalf.h
Eigen/src/Core/arch/CUDA/TypeCasting.h
Eigen/src/Core/arch/Default/Settings.h
Eigen/src/Core/arch/NEON/Complex.h
Eigen/src/Core/arch/NEON/MathFunctions.h
Eigen/src/Core/arch/NEON/PacketMath.h
Eigen/src/Core/arch/SSE/Complex.h
Eigen/src/Core/arch/SSE/MathFunctions.h
Eigen/src/Core/arch/SSE/PacketMath.h
Eigen/src/Core/arch/SSE/TypeCasting.h
Eigen/src/Core/arch/ZVector/Complex.h
Eigen/src/Core/arch/ZVector/MathFunctions.h
Eigen/src/Core/arch/ZVector/PacketMath.h
Eigen/src/Core/functors/AssignmentFunctors.h
Eigen/src/Core/functors/BinaryFunctors.h
Eigen/src/Core/functors/NullaryFunctors.h
Eigen/src/Core/functors/StlFunctors.h
Eigen/src/Core/functors/TernaryFunctors.h
Eigen/src/Core/functors/UnaryFunctors.h
Eigen/src/Core/products/GeneralBlockPanelKernel.h
Eigen/src/Core/products/GeneralMatrixMatrix.h
Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h
Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h
Eigen/src/Core/products/GeneralMatrixVector.h
Eigen/src/Core/products/GeneralMatrixVector_BLAS.h
Eigen/src/Core/products/Parallelizer.h
Eigen/src/Core/products/SelfadjointMatrixMatrix.h
Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h
Eigen/src/Core/products/SelfadjointMatrixVector.h
Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h
Eigen/src/Core/products/SelfadjointProduct.h
Eigen/src/Core/products/SelfadjointRank2Update.h
Eigen/src/Core/products/TriangularMatrixMatrix.h
Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h
Eigen/src/Core/products/TriangularMatrixVector.h
Eigen/src/Core/products/TriangularMatrixVector_BLAS.h
Eigen/src/Core/products/TriangularSolverMatrix.h
Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h
Eigen/src/Core/products/TriangularSolverVector.h
Eigen/src/Core/util/BlasUtil.h
Eigen/src/Core/util/Constants.h
Eigen/src/Core/util/DisableStupidWarnings.h
Eigen/src/Core/util/ForwardDeclarations.h
Eigen/src/Core/util/MKL_support.h
Eigen/src/Core/util/Macros.h
Eigen/src/Core/util/Memory.h
Eigen/src/Core/util/Meta.h
Eigen/src/Core/util/NonMPL2.h
Eigen/src/Core/util/ReenableStupidWarnings.h
Eigen/src/Core/util/StaticAssert.h
Eigen/src/Core/util/XprHelper.h
Eigen/src/Eigenvalues/ComplexEigenSolver.h
Eigen/src/Eigenvalues/ComplexSchur.h
Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h
Eigen/src/Eigenvalues/EigenSolver.h
Eigen/src/Eigenvalues/GeneralizedEigenSolver.h
Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h
Eigen/src/Eigenvalues/HessenbergDecomposition.h
Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
Eigen/src/Eigenvalues/RealQZ.h
Eigen/src/Eigenvalues/RealSchur.h
Eigen/src/Eigenvalues/RealSchur_LAPACKE.h
Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h
Eigen/src/Eigenvalues/Tridiagonalization.h
Eigen/src/Geometry/AlignedBox.h
Eigen/src/Geometry/AngleAxis.h
Eigen/src/Geometry/EulerAngles.h
Eigen/src/Geometry/Homogeneous.h
Eigen/src/Geometry/Hyperplane.h
Eigen/src/Geometry/OrthoMethods.h
Eigen/src/Geometry/ParametrizedLine.h
Eigen/src/Geometry/Quaternion.h
Eigen/src/Geometry/Rotation2D.h
Eigen/src/Geometry/RotationBase.h
Eigen/src/Geometry/Scaling.h
Eigen/src/Geometry/Transform.h
Eigen/src/Geometry/Translation.h
Eigen/src/Geometry/Umeyama.h
Eigen/src/Geometry/arch/Geometry_SSE.h
Eigen/src/Householder/BlockHouseholder.h
Eigen/src/Householder/Householder.h
Eigen/src/Householder/HouseholderSequence.h
Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h
Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h
Eigen/src/IterativeLinearSolvers/SolveWithGuess.h
Eigen/src/Jacobi/Jacobi.h
Eigen/src/LU/Determinant.h
Eigen/src/LU/FullPivLU.h
Eigen/src/LU/InverseImpl.h
Eigen/src/LU/PartialPivLU.h
Eigen/src/LU/PartialPivLU_LAPACKE.h
Eigen/src/LU/arch/Inverse_SSE.h
Eigen/src/MetisSupport/MetisSupport.h
Eigen/src/OrderingMethods/Amd.h
Eigen/src/OrderingMethods/Eigen_Colamd.h
Eigen/src/OrderingMethods/Ordering.h
Eigen/src/PaStiXSupport/PaStiXSupport.h
Eigen/src/PardisoSupport/PardisoSupport.h
Eigen/src/QR/ColPivHouseholderQR.h
Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h
Eigen/src/QR/CompleteOrthogonalDecomposition.h
Eigen/src/QR/FullPivHouseholderQR.h
Eigen/src/QR/HouseholderQR.h
Eigen/src/QR/HouseholderQR_LAPACKE.h
Eigen/src/SPQRSupport/SuiteSparseQRSupport.h
Eigen/src/SVD/BDCSVD.h
Eigen/src/SVD/JacobiSVD.h
Eigen/src/SVD/JacobiSVD_LAPACKE.h
Eigen/src/SVD/SVDBase.h
Eigen/src/SVD/UpperBidiagonalization.h
Eigen/src/SparseCholesky/SimplicialCholesky.h
Eigen/src/SparseCholesky/SimplicialCholesky_impl.h
Eigen/src/SparseCore/AmbiVector.h
Eigen/src/SparseCore/CompressedStorage.h
Eigen/src/SparseCore/ConservativeSparseSparseProduct.h
Eigen/src/SparseCore/MappedSparseMatrix.h
Eigen/src/SparseCore/SparseAssign.h
Eigen/src/SparseCore/SparseBlock.h
Eigen/src/SparseCore/SparseColEtree.h
Eigen/src/SparseCore/SparseCompressedBase.h
Eigen/src/SparseCore/SparseCwiseBinaryOp.h
Eigen/src/SparseCore/SparseCwiseUnaryOp.h
Eigen/src/SparseCore/SparseDenseProduct.h
Eigen/src/SparseCore/SparseDiagonalProduct.h
Eigen/src/SparseCore/SparseDot.h
Eigen/src/SparseCore/SparseFuzzy.h
Eigen/src/SparseCore/SparseMap.h
Eigen/src/SparseCore/SparseMatrix.h
Eigen/src/SparseCore/SparseMatrixBase.h
Eigen/src/SparseCore/SparsePermutation.h
Eigen/src/SparseCore/SparseProduct.h
Eigen/src/SparseCore/SparseRedux.h
Eigen/src/SparseCore/SparseRef.h
Eigen/src/SparseCore/SparseSelfAdjointView.h
Eigen/src/SparseCore/SparseSolverBase.h
Eigen/src/SparseCore/SparseSparseProductWithPruning.h
Eigen/src/SparseCore/SparseTranspose.h
Eigen/src/SparseCore/SparseTriangularView.h
Eigen/src/SparseCore/SparseUtil.h
Eigen/src/SparseCore/SparseVector.h
Eigen/src/SparseCore/SparseView.h
Eigen/src/SparseCore/TriangularSolver.h
Eigen/src/SparseLU/SparseLU.h
Eigen/src/SparseLU/SparseLUImpl.h
Eigen/src/SparseLU/SparseLU_Memory.h
Eigen/src/SparseLU/SparseLU_Structs.h
Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h
Eigen/src/SparseLU/SparseLU_Utils.h
Eigen/src/SparseLU/SparseLU_column_bmod.h
Eigen/src/SparseLU/SparseLU_column_dfs.h
Eigen/src/SparseLU/SparseLU_copy_to_ucol.h
Eigen/src/SparseLU/SparseLU_gemm_kernel.h
Eigen/src/SparseLU/SparseLU_heap_relax_snode.h
Eigen/src/SparseLU/SparseLU_kernel_bmod.h
Eigen/src/SparseLU/SparseLU_panel_bmod.h
Eigen/src/SparseLU/SparseLU_panel_dfs.h
Eigen/src/SparseLU/SparseLU_pivotL.h
Eigen/src/SparseLU/SparseLU_pruneL.h
Eigen/src/SparseLU/SparseLU_relax_snode.h
Eigen/src/SparseQR/SparseQR.h
Eigen/src/StlSupport/StdDeque.h
Eigen/src/StlSupport/StdList.h
Eigen/src/StlSupport/StdVector.h
Eigen/src/StlSupport/details.h
Eigen/src/SuperLUSupport/SuperLUSupport.h
Eigen/src/UmfPackSupport/UmfPackSupport.h
Eigen/src/misc/Image.h
Eigen/src/misc/Kernel.h
Eigen/src/misc/RealSvd2x2.h
Eigen/src/misc/blas.h
Eigen/src/misc/lapack.h
Eigen/src/misc/lapacke.h
Eigen/src/misc/lapacke_mangling.h
Eigen/src/plugins/ArrayCwiseBinaryOps.h
Eigen/src/plugins/ArrayCwiseUnaryOps.h
Eigen/src/plugins/BlockMethods.h
Eigen/src/plugins/CommonCwiseBinaryOps.h
Eigen/src/plugins/CommonCwiseUnaryOps.h
Eigen/src/plugins/MatrixCwiseBinaryOps.h
Eigen/src/plugins/MatrixCwiseUnaryOps.h
)
find_library(ZLIB z HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT ZLIB)
message(FATAL_ERROR "libz library not found")
endif()
find_library(CURLLIB curl HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT CURLLIB)
message(FATAL_ERROR "libcurl library not found")
endif()
find_package (BZip2)
if (NOT BZIP2_FOUND)
message(FATAL_ERROR "libbz2 library not found")
else()
include_directories(${BZIP2_INCLUDE_DIRS})
set(BZIP2 ${BZIP2_LIBRARIES})
endif()
find_library(LZMA lzma HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT LZMA)
message(WARNING "liblzma library not found, if you specified --disable-lzma when compiling libhts, please ignore this warning")
set(LZMA "")
else()
set(LZMA ${LZMA_LIBRARIES})
endif()
find_library(CRYPTOLIB crypto HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
if(NOT CRYPTOLIB)
message(FATAL_ERROR "libcrypto library not found")
endif()
find_package(Threads REQUIRED)
find_package(OpenSSL REQUIRED)
target_link_libraries(cramore ${HTS_LIBRARIES} ${ZLIB} ${BZIP2} ${LZMA} ${CURLLIB} ${CRYPTOLIB} ${CMAKE_THREAD_LIBS_INIT})
install(TARGETS cramore RUNTIME DESTINATION bin)