{"commit":"cafc0e5b026b24e0a331cc71a86e7e47a493b6f4","old_file":"PrelimNRSA\/HyPhyMaterials\/run.bf","new_file":"PrelimNRSA\/HyPhyMaterials\/run.bf","old_contents":"\nglobal w;\nglobal t;\nglobal k;\n\n\n\nLIKELIHOOD_FUNCTION_OUTPUT = 1;\nRANDOM_STARTING_PERTURBATIONS = 1;\n\n\n\/* Include relevant functions *\/\n#include \"matrices.mdl\"; \/\/rate matrices\n#include \"GY94_Header.ibf\";\n\n\/* Read in the data *\/\nDataSet\traw_data = ReadDataFile(\"temp.fasta\");\n\n\/* Filter the data to find and remove any stop codons*\/\nDataSetFilter   filt_data = CreateFilter(raw_data,3,\"\", \"\",\"TAA,TAG,TGA\");\n\n\/* Collect observed frequencies into vectors *\/\nHarvestFrequencies(observedFreq_data,filt_data,3,1,1);\n\n\n\/* Get the codon frequencies from the nucleotide frequency vectors *\/\ncodonFreq_data = BuildCodonFrequencies(observedFreq_data);\n\n\/* Define the model and tree *\/\nModel MyModel = (GY94, codonFreq_data, 1);\nUseModel (USE_NO_MODEL);\nUseModel(MyModel);\nTree    Tree01 = DATAFILE_TREE;\n\n\n\/*COMPUTE LIKELIHOODS*\/\n\nLikelihoodFunction  LikFn2 = (filt_data, Tree01);\n\nOptimize (paramValues2, LikFn2);\nfprintf (stdout, LikFn2);\n","new_contents":"\n\nglobal w;\nglobal t;\nglobal k;\n\n\nLIKELIHOOD_FUNCTION_OUTPUT = 1;\nRANDOM_STARTING_PERTURBATIONS = 1;\n\n\n\/* Include relevant functions *\/\n#include \"matrices_fix_k.mdl\"; \/\/rate matrices\n#include \"GY94_Header.ibf\";\n\n\/* Read in the data *\/\nDataSet\traw_data = ReadDataFile(\"temp.fasta\");\n\n\/* Filter the data to find and remove any stop codons*\/\nDataSetFilter   filt_data = CreateFilter(raw_data,3,\"\", \"\",\"TAA,TAG,TGA\");\n\n\/* Collect observed frequencies into vectors *\/\nHarvestFrequencies(observedFreq_data,filt_data,3,1,1);\n\n\n\/* Get the codon frequencies from the nucleotide frequency vectors *\/\ncodonFreq_data = BuildCodonFrequencies(observedFreq_data);\n\n\/* Define the model and tree *\/\nModel MyModel = (GY94, codonFreq_data, 1);\nUseModel (USE_NO_MODEL);\nUseModel(MyModel);\nTree    Tree01 = DATAFILE_TREE;\n\n\n\/*COMPUTE LIKELIHOODS*\/\n\nLikelihoodFunction  LikFn2 = (filt_data, Tree01);\n\nOptimize (paramValues2, LikFn2);\nfprintf (stdout, LikFn2);\n","subject":"Save the correct hyphy materials","message":"Save the correct hyphy materials\n","lang":"Brainfuck","license":"bsd-2-clause","repos":"SimonGreenhill\/pyvolve,SimonGreenhill\/pyvolve"}
{"commit":"4e2b164c927dcb9b7f6f298b0d1c1e67f7e668a3","old_file":"brainfuck\/fizzbuzz.bf","new_file":"brainfuck\/fizzbuzz.bf","old_contents":"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ f\n>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ i\n>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ z\n>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ b\n>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ u\n>++++++++++ lf\n\n>\n++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ set loop num\n\n> leave 0 for exit flag\n\n>\n+++ set cycle num\n\n>>>>\n+++++ set second cycle num\n<<<<\n\n<< back to cycle\n[\n  >> cycle check\n  [\n    - decrement cycle num\n\n    >+>+<< sets zero flags bit to 1\n    [\n      >[-]>[-]<< sets temp bit to 0 in case it's still not 0\n      < go to exit this is why we need 2 zero\n    ]\n\n    >> check if zero flag is on\n    [\n      <<<<<<<<<<.>.>..>>>>>>>> fizz\n\n      <<+++>> restore cycle number\n      [-]<[-] zero the flags\n    ]\n    < back to cycle num\n    < back to exit flag\n  ]\n\n  >>>>> cycle check\n  [\n    - decrement cycle num\n\n    >+>+<< sets zero flags bit to 1\n    [\n      >[-]>[-]<< sets temp bit to 0 in case it's still not 0\n      < go to exit this is why we need 2 zero\n    ]\n\n    >> check if zero flag is on\n    [\n      <<<<<<<<<<<.>.<<..>>>>>>>>>>>> buzz\n\n      <<+++++>> restore cycle number\n      [-]<[-] zero the flags\n    ]\n    < back to cycle num\n    < back to exit flag\n  ]\n  <<<<\n\n  <<.>> new line\n\n  <-\n]\n","new_contents":"+++++++++++++++++++++++++++++++++++++++++++++ empty line sign\n>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ f\n>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ i\n>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ z\n>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ b\n>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ u\n>++++++++++ lf\n\n>\n++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ set loop num\n\n> leave 0 for exit flag\n\n>>>\n+++ set cycle num\n\n>>>>\n+++++ set second cycle num\n<<<<<<\n\n<< back to cycle\n[\n  >+>+ set else flag (when no cycle is zero)\n\n  >> cycle check\n  [\n    - decrement cycle num\n\n    >+>+<< sets zero flags bit to 1\n    [\n      >[-]>[-]<< sets temp bit to 0 in case it's still not 0\n      < go to exit this is why we need 2 zero\n    ]\n\n    >> check if zero flag is on\n    [\n      <<<<<<<<<<<<.>.>..>>>>>>>>>> fizz\n\n      <<<<[-]<[-]>>>>> remove else flags\n\n      <<+++>> restore cycle number\n      [-]<[-] zero the flags\n    ]\n    < back to cycle num\n    < back to exit flag\n  ]\n\n  >>>>> cycle check\n  [\n    - decrement cycle num\n\n    >+>+<< sets zero flags bit to 1\n    [\n      >[-]>[-]<< sets temp bit to 0 in case it's still not 0\n      < go to exit this is why we need 2 zero\n    ]\n\n    >> check if zero flag is on\n    [\n      <<<<<<<<<<<<<.>.<<..>>>>>>>>>>>>>> buzz\n\n      <<<<<<<<[-]<[-]>>>>>>>>> remove else flags\n\n      <<+++++>> restore cycle number\n      [-]<[-] zero the flags\n    ]\n    < back to cycle num\n    < back to exit flag\n  ]\n  <<<<<<< back to loop\n\n  >\n  [\n    <<<<<<<<.>>>>>>>> new line\n    [-]\n  ]\n  <\n\n  <.>\n\n  - decrement loop\n]\n","subject":"Add filling char to bf","message":"Add filling char to bf\n","lang":"Brainfuck","license":"apache-2.0","repos":"itarato\/fizzbuzz,itarato\/fizzbuzz,itarato\/fizzbuzz,itarato\/fizzbuzz,itarato\/fizzbuzz,itarato\/fizzbuzz,itarato\/fizzbuzz,itarato\/fizzbuzz,itarato\/fizzbuzz"}