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        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
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       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
prime-phylo-1.0.11/CMakeLists.txt-22-
prime-phylo-1.0.11/CMakeLists.txt:23:include(${CMAKE_SOURCE_DIR}/cmake/macro.cmake)
prime-phylo-1.0.11/CMakeLists.txt-24-
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prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh-21-  //! \f],
prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:22:  //! where \f$ \alpha = mean - \sqrt{3 variance} \f$, 
prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh-23-  //!   \f$ \beta = mean + \sqrt{3 variance} \f$  
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prime-phylo-1.0.11/src/cxx/tools/reconcile/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/reconcile/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/reroot/CMakeLists.txt-1-
prime-phylo-1.0.11/src/cxx/tools/reroot/CMakeLists.txt:2:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/reroot/CMakeLists.txt-3-
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prime-phylo-1.0.11/src/cxx/tools/showtree2/CMakeLists.txt-1-
prime-phylo-1.0.11/src/cxx/tools/showtree2/CMakeLists.txt:2:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/showtree2/CMakeLists.txt-3-
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prime-phylo-1.0.11/src/cxx/tools/showtree/CMakeLists.txt-1-
prime-phylo-1.0.11/src/cxx/tools/showtree/CMakeLists.txt:2:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/showtree/CMakeLists.txt-3-
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prime-phylo-1.0.11/src/cxx/tools/kambo/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/kambo/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/prime_generateTree/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/prime_generateTree/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/orthoFromOldPrIME/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/orthoFromOldPrIME/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/prime_s/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/prime_s/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/lsdcombine/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/lsdcombine/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/getwgd/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/getwgd/CMakeLists.txt-2-#does not compile right now
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prime-phylo-1.0.11/src/cxx/tools/readReconciliation/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/readReconciliation/CMakeLists.txt-2-#does not compile right now
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prime-phylo-1.0.11/src/cxx/tools/compute_ortho/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/compute_ortho/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/genGSR/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/genGSR/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/ortho_true_vertices/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/ortho_true_vertices/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/treesize/CMakeLists.txt-1-
prime-phylo-1.0.11/src/cxx/tools/treesize/CMakeLists.txt:2:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/treesize/CMakeLists.txt-3-
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prime-phylo-1.0.11/src/cxx/tools/chainsaw/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/chainsaw/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/fileformatconversion/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/fileformatconversion/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/CMakeLists.txt-1-
prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/CMakeLists.txt:2:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/CMakeLists.txt-3-
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prime-phylo-1.0.11/src/cxx/test_applications/beep_generateTree/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/test_applications/beep_generateTree/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/test_applications/test_PhyloDAG/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/test_applications/test_PhyloDAG/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/test_applications/beep_generateSeqData/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/test_applications/beep_generateSeqData/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/primeGEMrec/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/primeGEMrec/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/primeDLRS/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/primeDLRS/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/primeCT/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/primeCT/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/mapdp/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/mapdp/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/primeRecon/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/primeRecon/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/prime_enumerate_reconciliations/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/prime_enumerate_reconciliations/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/primeDUP/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/primeDUP/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/primeDLRS-esjolund/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/primeDLRS-esjolund/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/cxx/applications/primeGEM/CMakeLists.txt:1:include(${CMAKE_SOURCE_DIR}/src/cxx/cmake-include.txt)
prime-phylo-1.0.11/src/cxx/applications/primeGEM/CMakeLists.txt-2-
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prime-phylo-1.0.11/src/perl/mcmc_analysis-833-  close(F);
prime-phylo-1.0.11/src/perl/mcmc_analysis:834:  system('gnuplot', $plotfile);
prime-phylo-1.0.11/src/perl/mcmc_analysis-835-  open(T, "<$texfile") or die "No LaTeX file produced by gnuplot!";