├── doc ├── CLL077_whole.png ├── CLL077_whole.sol └── CLL077_whole.dot ├── src ├── config.h.in ├── solver.cpp ├── solver.h ├── constructancestrymatrix.cpp ├── realmatrix.h ├── matrix.cpp ├── probcomparison.h ├── realintervalmatrix.cpp ├── matrix.h ├── realmatrix.cpp ├── utils.h ├── machinainput.cpp ├── visualizesolution.cpp ├── comparison.h ├── cluster.cpp ├── solutiongraph.h ├── intmaxilpsolver.h ├── maxsolution.h ├── baseancestrygraph.cpp ├── readcountmatrix.h ├── ppmatrix.cpp ├── realintervalmatrix.h ├── ppmatrix.h ├── analysesolution.cpp └── probcomparison.cpp ├── .gitignore ├── data ├── real │ ├── CLL006_whole.txt │ ├── CLL006_deep.txt │ ├── CLL077_whole.txt │ ├── CLL077_deep.txt │ ├── CLL003_whole.txt │ ├── README.md │ ├── CLL003_deep.txt │ ├── 283_whole.txt │ ├── 283_deep.txt │ ├── 292_whole.txt │ ├── 292_deep.txt │ ├── RMH002.txt │ └── EV003.txt └── simulated │ ├── Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed │ ├── sim_8.input │ ├── sim_6.input │ ├── sim_5.input │ ├── sim_3.input │ ├── sim_1.input │ ├── sim_9.input │ ├── sim_0.input │ ├── sim_2.input │ ├── sim_4.input │ └── sim_7.input │ ├── Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed │ ├── sim_6.input │ ├── sim_5.input │ ├── sim_3.input │ ├── sim_4.input │ ├── sim_2.input │ ├── sim_1.input │ ├── sim_8.input │ ├── sim_7.input │ ├── sim_0.input │ └── sim_9.input │ ├── Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed │ ├── sim_6.input │ ├── sim_9.input │ ├── sim_7.input │ ├── sim_4.input │ ├── sim_2.input │ ├── sim_0.input │ ├── sim_3.input │ ├── sim_8.input │ ├── sim_1.input │ └── sim_5.input │ └── Cov_100_Samples_5_Mut_100_Clone_10_PCR_Removed │ ├── sim_6.input │ ├── sim_2.input │ ├── sim_7.input │ ├── sim_9.input │ ├── sim_3.input │ ├── sim_4.input │ ├── sim_5.input │ └── sim_0.input └── LICENSE.txt /doc/CLL077_whole.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphael-group/AncesTree/HEAD/doc/CLL077_whole.png -------------------------------------------------------------------------------- /src/config.h.in: -------------------------------------------------------------------------------- 1 | #ifndef CONFIG_H 2 | #define CONFIG_H 3 | 4 | #define ANCESTREE_VERSION @ANCESTREE_VERSION@ 5 | 6 | #endif // CONFIG_H 7 | -------------------------------------------------------------------------------- /src/solver.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * solver.cpp 3 | * 4 | * Created on: 22-dec-2014 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "solver.h" 9 | 10 | namespace vaff { 11 | 12 | Solver::Solver(const RealMatrix& F) 13 | : _F(F) 14 | { 15 | } 16 | 17 | Solver::~Solver() 18 | { 19 | } 20 | 21 | } // namespace vaff 22 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Compiled Object files 2 | *.slo 3 | *.lo 4 | *.o 5 | *.obj 6 | 7 | # Precompiled Headers 8 | *.gch 9 | *.pch 10 | 11 | # Compiled Dynamic libraries 12 | *.so 13 | *.dylib 14 | *.dll 15 | 16 | # Fortran module files 17 | *.mod 18 | 19 | # Compiled Static libraries 20 | *.lai 21 | *.la 22 | *.a 23 | *.lib 24 | 25 | # Executables 26 | *.exe 27 | *.out 28 | *.app 29 | 30 | # Mac stuff 31 | .DS_Store 32 | 33 | # Python things 34 | *.pyc 35 | 36 | # Build directory 37 | build/ 38 | src/config.h 39 | -------------------------------------------------------------------------------- /src/solver.h: -------------------------------------------------------------------------------- 1 | /* 2 | * solver.h 3 | * 4 | * Created on: 22-dec-2014 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef SOLVER_H 9 | #define SOLVER_H 10 | 11 | #include "utils.h" 12 | #include "solution.h" 13 | 14 | namespace vaff { 15 | 16 | class Solver 17 | { 18 | public: 19 | Solver(const RealMatrix& V); 20 | 21 | virtual ~Solver(); 22 | 23 | virtual bool solve(Solution& solution) = 0; 24 | 25 | protected: 26 | const RealMatrix& _F; 27 | }; 28 | 29 | } // namespace vaff 30 | 31 | #endif // SOLVER_H 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /data/real/CLL006_whole.txt: -------------------------------------------------------------------------------- 1 | gene_id a a b b c c d d e e 2 | ARHGAP29 22 9 15 17 11 7 20 16 20 18 3 | C3orf43 16 13 28 17 35 24 21 22 30 33 4 | CNOT7 29 17 27 22 21 24 25 22 15 24 5 | IRF4 36 4 30 10 33 8 25 11 22 13 6 | KIAA0182 28 28 18 13 15 15 19 20 24 21 7 | KIAA0319L 35 7 39 8 20 14 35 12 30 16 8 | KLHL4 1 16 3 17 0 15 2 16 1 25 9 | LRRC37B 45 5 33 5 18 10 19 14 26 15 10 | MAP4 27 16 22 18 23 18 30 14 27 17 11 | MED12 2 20 0 17 0 21 1 19 0 19 12 | PCLO 31 14 32 12 37 20 28 16 30 27 13 | PILRB 26 17 25 22 24 13 13 13 18 20 14 | RBPJ 35 0 36 1 23 1 26 4 49 1 15 | SIK1 20 17 18 18 17 15 28 18 20 23 16 | TMPRSS9 21 21 11 14 20 18 17 13 29 17 17 | U2AF1 24 21 30 16 18 14 24 24 23 21 18 | -------------------------------------------------------------------------------- /data/real/CLL006_deep.txt: -------------------------------------------------------------------------------- 1 | gene_id a a b b c c d d e e 2 | ARHGAP29 66023 60732 50883 49586 62757 59184 36056 35207 58777 56640 3 | IRF4 93057 13659 61406 21773 72640 11159 61648 24792 54961 29646 4 | KIAA0182 31531 40690 40281 44182 18089 19321 34256 38794 36473 40396 5 | KIAA0319L 94954 21432 74636 31882 67529 15742 42328 23824 59678 34787 6 | KLHL4 9653 103122 2300 76787 4506 80201 3559 88517 3695 92154 7 | MED12 9072 118007 2953 109099 4140 82486 5150 131905 5270 180700 8 | PILRB 36288 37719 28055 30095 26648 29638 35692 40887 26492 28352 9 | RBPJ 75935 891 106216 4923 153378 2011 115054 8251 112006 7954 10 | SIK1 28543 23386 31070 33607 57616 58849 34454 33939 40929 38859 11 | U2AF1 54447 28334 39896 33474 60454 32440 63950 56434 48658 40853 12 | -------------------------------------------------------------------------------- /data/real/CLL077_whole.txt: -------------------------------------------------------------------------------- 1 | gene_id a a b b c c d d e e 2 | BCL2L13 20 22 15 6 19 22 31 21 28 15 3 | COL24A1 43 0 41 0 40 0 50 5 37 7 4 | DAZAP1 21 9 11 7 13 11 28 9 35 4 5 | DDX1 58 0 34 0 39 4 54 4 43 9 6 | EXOC6B 33 19 36 16 22 13 34 10 38 4 7 | GHDC 24 21 23 7 21 14 31 13 28 1 8 | GPR158 29 22 14 11 23 22 24 21 26 11 9 | HMCN1 36 0 40 0 54 0 39 7 41 9 10 | IRF2BP2 21 16 13 11 11 13 24 16 29 16 11 | KLHDC2 38 0 38 1 36 1 52 6 41 9 12 | LRRC16A 46 10 23 8 39 6 34 7 34 0 13 | MAP2K1 36 0 19 0 26 0 38 6 23 10 14 | NAMPTL 23 23 21 19 14 32 27 29 29 20 15 | NOD1 38 0 25 0 28 0 43 2 32 7 16 | OCA2 24 13 25 12 22 9 25 16 29 8 17 | PLA2G16 32 21 15 6 31 16 38 24 51 3 18 | SAMHD1 6 46 5 48 0 35 4 59 15 24 19 | SLC12A1 35 17 18 16 21 9 29 20 42 9 20 | ZFHX4 48 0 38 0 32 0 38 3 29 8 21 | ZNF566 39 0 25 0 43 0 58 0 40 7 22 | -------------------------------------------------------------------------------- /data/real/CLL077_deep.txt: -------------------------------------------------------------------------------- 1 | gene_id a a b b c c d d e e 2 | BCL2L13 103227 88237 109253 110443 92745 95955 107526 99165 161950 78504 3 | COL24A1 144675 371 166807 2251 139149 3476 139477 11087 116902 24874 4 | DAZAP1 66924 40996 42934 26647 52929 35225 65298 30848 70111 8972 5 | EXOC6B 141110 77824 131091 85138 122161 77934 145782 68329 191685 24002 6 | GHDC 87368 47334 73334 45895 97303 66701 97512 47403 114085 16734 7 | GPR158 44553 34183 41199 37812 31430 31788 37319 34419 51335 22502 8 | HMCN1 131456 471 116533 1586 112512 2341 97526 6647 79443 14522 9 | KLHDC2 177281 891 165542 2509 151722 3139 154556 11277 92636 16352 10 | LRRC16A 166260 33114 168945 59394 184363 61346 176093 42417 206836 10346 11 | MAP2K1 115796 446 84349 1405 100745 2331 91947 7357 116342 21929 12 | NAMPTL 77327 72896 86968 86651 53693 58490 64079 63014 60855 29711 13 | NOD1 89298 202 85427 1046 92327 1649 86933 5624 78844 12481 14 | OCA2 97312 53930 86726 57202 90173 56659 113895 54738 141769 16557 15 | PLA2G16 115049 65807 110108 77211 98672 68209 137336 69281 155411 21064 16 | SAMHD1 25098 221550 13135 227255 2434 188610 15070 239504 82680 132810 17 | SLC12A1 100226 85098 87675 82118 80349 72361 95477 82828 121566 45217 18 | -------------------------------------------------------------------------------- /data/real/CLL003_whole.txt: -------------------------------------------------------------------------------- 1 | gene_id a a b b c c d d e e 2 | ADAD1 16 22 30 18 18 11 17 20 19 23 3 | AMTN 24 9 14 16 37 3 46 0 25 0 4 | APBB2 24 19 21 17 33 2 40 0 44 0 5 | ASXL1 39 1 38 2 18 13 13 27 18 17 6 | ATM 6 31 3 16 24 1 26 0 19 0 7 | BPIL2 33 24 24 27 49 3 54 0 24 0 8 | CHRNB2 26 0 32 0 31 9 27 20 19 14 9 | CHTF8 15 9 14 7 19 4 13 10 17 9 10 | FAT3 39 0 34 0 35 6 31 19 23 12 11 | FCGBP 22 16 19 15 32 2 44 0 35 0 12 | HERC2 30 16 20 13 27 17 15 34 17 15 13 | IL11RA 12 19 17 20 18 8 19 29 15 18 14 | MTUS1 27 15 27 18 44 2 21 1 25 0 15 | MUC16 13 18 15 13 25 14 18 16 15 12 16 | MUSK 44 2 37 0 29 6 23 19 15 13 17 | NFATC1 34 20 15 12 37 2 45 0 37 0 18 | NLRP3 21 25 17 13 20 14 22 25 13 20 19 | NPY_1 39 0 28 0 30 10 22 12 18 14 20 | NPY_2 42 0 30 0 29 11 23 12 18 14 21 | NRG3 42 0 34 0 27 6 26 27 13 19 22 | PLEKHG5 25 20 19 18 37 3 44 0 23 0 23 | RPGRIP1 22 21 16 17 13 15 22 16 16 13 24 | SEMA3E 53 5 45 2 39 6 25 24 22 36 25 | SF3B1 22 22 12 21 25 10 26 18 13 19 26 | SHROOM1 22 28 13 19 25 6 24 19 13 10 27 | SLC9A11 16 20 18 25 26 16 32 32 14 27 28 | SLITRK4 27 0 20 0 9 8 2 18 0 16 29 | SPTAN1 26 16 24 18 34 4 47 0 30 0 30 | TRIM58 15 19 20 16 28 18 28 27 19 21 31 | ZNF534 43 3 48 3 37 4 26 17 18 11 32 | -------------------------------------------------------------------------------- /data/real/README.md: -------------------------------------------------------------------------------- 1 | ##Datasets 2 | --- 3 | 4 | ### Format 5 | 6 | Text files, tab separated. First line contains sample headers. First column contains gene ids. Then every consecutive pair of columns contains read counts for reference and alternate. 7 | 8 | ####Kidney [Gerlinger et al. (2014)] 9 | 10 | doi:10.1038/ng.2891 11 | 12 | * EV003.txt 13 | * EV005.txt 14 | * EV006.txt 15 | * EV007.txt 16 | * RK26.txt 17 | * RMH002.txt 18 | * RMH004.txt 19 | * RMH008.txt 20 | 21 | ####Lung cancer [de Bruin et al. (2014)] 22 | 23 | doi:10.1126/science.1253462 24 | 25 | * 270_deep.txt 26 | * 270_whole.txt 27 | * 283_deep.txt 28 | * 283_whole.txt 29 | * 292_deep.txt 30 | * 292_whole.txt 31 | * 317_deep.txt 32 | * 317_whole.txt 33 | * 324_deep.txt 34 | * 324_whole.txt 35 | * 330_deep.txt 36 | * 330_whole.txt 37 | * 339_deep.txt 38 | * 339_whole.txt 39 | * 356_deep.txt 40 | * 356_whole.txt 41 | * 472_deep.txt 42 | * 472_whole.txt 43 | * 4990_deep.txt 44 | * 4990_whole.txt 45 | * 499_deep.txt 46 | * 499_whole.txt 47 | 48 | ####CLL [Schuh et al. (2012)] 49 | 50 | doi:10.1182/blood-2012-05-433540 51 | 52 | * CLL003_deep.txt 53 | * CLL003_whole.txt 54 | * CLL006_deep.txt 55 | * CLL006_whole.txt 56 | * CLL077_deep.txt 57 | * CLL077_whole.txt 58 | -------------------------------------------------------------------------------- /data/real/CLL003_deep.txt: -------------------------------------------------------------------------------- 1 | gene_id a a b b c c d d e e 2 | ADAD1 52413 52442 46521 46444 90519 44095 55248 50480 50791 50214 3 | AMTN 8618 6622 7892 6933 15141 975 14501 45 15223 37 4 | APBB2 41273 29394 37661 33730 59192 4112 64202 131 65198 125 5 | ASXL1 68541 4041 56696 2544 55552 23617 38370 37246 38236 41221 6 | ATM 19418 57014 12953 68604 46148 5183 90346 242 100250 321 7 | BPIL2 60361 39019 41885 31157 82300 5224 79096 150 89711 223 8 | CHRNB2 66715 81 47970 328 45864 13268 37054 32461 34171 36523 9 | CHTF8 61220 51520 63116 61061 108718 50527 77450 61186 72265 64850 10 | FAT3 86163 39 83302 372 52873 16610 42240 32888 39421 36820 11 | HERC2 22636 20014 18338 17993 27955 14088 23033 18078 20191 19353 12 | IL11RA 66830 50124 61270 53084 80584 36376 58443 46238 57205 47778 13 | MTUS1 59746 39685 51722 45533 76146 6878 97796 498 98421 281 14 | MUSK 20887 1006 13517 592 11145 4578 8874 7798 8400 8259 15 | NPY 45544 42 47549 209 41928 10337 30054 22337 25929 21358 16 | NRG3 57479 58 53871 304 45939 13618 29345 24075 28306 25070 17 | PLEKHG5 22318 16295 19476 15207 37953 2203 35666 75 40863 146 18 | SEMA3E 26300 1320 26786 858 22009 8095 14898 12293 13955 12957 19 | SF3B1 45001 41887 43873 44071 56080 27117 56217 47852 46240 43946 20 | SHROOM1 76030 71722 82913 82740 96239 46660 87811 73472 70865 67394 21 | SPTAN1 32026 21414 30511 25874 58620 3605 52513 132 55831 108 22 | -------------------------------------------------------------------------------- /src/constructancestrymatrix.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * print_max_solution.cpp 3 | * 4 | * Created on: 10-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "utils.h" 9 | #include "readcountmatrix.h" 10 | #include "ancestrymatrix.h" 11 | #include 12 | #include 13 | 14 | using namespace vaff; 15 | 16 | void printUsage(const char* argv0, std::ostream& out) 17 | { 18 | out << "Usage: " << argv0 << " where" << std::endl 19 | << " is the input file containing read counts\n" 20 | << " 0 for minimum" << std::endl; 21 | } 22 | 23 | int main(int argc, char** argv) 24 | { 25 | if (argc != 3) 26 | { 27 | printUsage(argv[0], std::cerr); 28 | return 1; 29 | } 30 | 31 | std::string filename = argv[1]; 32 | 33 | ReadCountMatrix R; 34 | if (filename != "-") 35 | { 36 | std::ifstream in(filename.c_str()); 37 | if (!in.good()) 38 | { 39 | std::cerr << "Error: failed to open '" << argv[1] << "' for reading" << std::endl; 40 | return 1; 41 | } 42 | in >> R; 43 | in.close(); 44 | } 45 | else 46 | { 47 | std::cin >> R; 48 | } 49 | 50 | int order = atoi(argv[2]); 51 | if (!(0 <= order && order < R.getNrCols())) 52 | { 53 | std::cerr << "Error: order has to be in [0, " << R.getNrCols() << "]" << std::endl; 54 | return 1; 55 | } 56 | 57 | AncestryMatrix M(R, order); 58 | std::cout << M; 59 | 60 | return 0; 61 | } -------------------------------------------------------------------------------- /src/realmatrix.h: -------------------------------------------------------------------------------- 1 | /* 2 | * realmatrix.h 3 | * 4 | * Created on: 22-dec-2014 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef REALMATRIX_H 9 | #define REALMATRIX_H 10 | 11 | #include "matrix.h" 12 | #include "utils.h" 13 | 14 | namespace vaff { 15 | 16 | class RealMatrix : public Matrix 17 | { 18 | public: 19 | RealMatrix(); 20 | 21 | RealMatrix(int m, int n); 22 | 23 | const StlDoubleMatrix& getMatrix() const 24 | { 25 | return _C; 26 | } 27 | 28 | double operator()(int row, int col) const 29 | { 30 | assert(0 <= row && row < _m); 31 | assert(0 <= col && col < _n); 32 | 33 | return _C[row][col]; 34 | } 35 | 36 | void set(int row, int col, double val) 37 | { 38 | assert(0 <= row && row < _m); 39 | assert(0 <= col && col < _n); 40 | 41 | _C[row][col] = val; 42 | } 43 | 44 | bool operator==(const RealMatrix& other) const 45 | { 46 | return _m == other._m && _n == other._n && _C == other._C; 47 | } 48 | 49 | bool operator!=(const RealMatrix& other) const 50 | { 51 | return !this->operator==(other); 52 | } 53 | 54 | RealMatrix subMatrix(const StlIntVector& columns) const; 55 | 56 | friend std::ostream& operator<<(std::ostream& out, 57 | const RealMatrix& matrix); 58 | 59 | friend std::istream& operator>>(std::istream& in, 60 | RealMatrix& matrix); 61 | 62 | protected: 63 | StlDoubleMatrix _C; 64 | }; 65 | 66 | } // namespace vaff 67 | 68 | #endif // REALMATRIX_H 69 | -------------------------------------------------------------------------------- /doc/CLL077_whole.sol: -------------------------------------------------------------------------------- 1 | 1 #sols 2 | 3 | 5 #observed F 4 | 20 5 | 0.52381 0 0.3 0 0.365385 0.466667 0.431373 0 0.432432 0 0.178571 0 0.5 0 0.351351 0.396226 0.884615 0.326923 0 0 6 | 0.285714 0 0.388889 0 0.307692 0.233333 0.44 0 0.458333 0.025641 0.258065 0 0.475 0 0.324324 0.285714 0.90566 0.470588 0 0 7 | 0.536585 0 0.458333 0.0930233 0.371429 0.4 0.488889 0 0.541667 0.027027 0.133333 0 0.695652 0 0.290323 0.340426 1 0.3 0 0 8 | 0.403846 0.0909091 0.243243 0.0689655 0.227273 0.295455 0.466667 0.152174 0.4 0.103448 0.170732 0.136364 0.517857 0.0444444 0.390244 0.387097 0.936508 0.408163 0.0731707 0 9 | 0.348837 0.159091 0.102564 0.173077 0.0952381 0.0344828 0.297297 0.18 0.355556 0.18 0 0.30303 0.408163 0.179487 0.216216 0.0555556 0.615385 0.176471 0.216216 0.148936 10 | 11 | a b c d e 12 | BCL2L13 COL24A1 DAZAP1 DDX1 EXOC6B GHDC GPR158 HMCN1 IRF2BP2 KLHDC2 LRRC16A MAP2K1 NAMPTL NOD1 OCA2 PLA2G16 SAMHD1 SLC12A1 ZFHX4 ZNF566 13 | 14 | 5 #U 15 | 5 16 | 0.507722 0 0.357143 0 0 17 | 0.39941 0 0.516129 0 0.00112769 18 | 0.546206 0 0.266667 0.186047 0.00108059 19 | 0.138787 0 0.341463 0.137931 0.181818 20 | 0 0.112467 0 0.23967 0.358974 21 | 5 #B 22 | 5 23 | 1 0 0 0 0 24 | 1 1 0 0 0 25 | 1 0 1 0 0 26 | 1 0 0 1 0 27 | 1 0 0 0 1 28 | 29 | 1 0.988261 0.936396 0.978667 0.981861 30 | 5 #inferred F 31 | 5 32 | 0.432432 0 0.178571 0 0 33 | 0.458333 0 0.258065 0 0.000563846 34 | 0.5 0 0.133333 0.0930233 0.000540297 35 | 0.4 0 0.170732 0.0689655 0.0909091 36 | 0.355556 0.0562334 0 0.119835 0.179487 37 | 38 | a b c d e 39 | 8;6 19 10 3 18;13;9;7;1 40 | 41 | -------------------------------------------------------------------------------- /src/matrix.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * matrix.cpp 3 | * 4 | * Created on: 22-dec-2014 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "matrix.h" 9 | #include "utils.h" 10 | #include 11 | #include 12 | #include 13 | #include 14 | 15 | namespace vaff { 16 | 17 | Matrix::Matrix() 18 | : _m(0) 19 | , _n(0) 20 | , _rowLabel() 21 | , _colLabel() 22 | , _labelsSet(false) 23 | { 24 | } 25 | 26 | Matrix::Matrix(int m, int n) 27 | : _m(m) 28 | , _n(n) 29 | , _rowLabel(m, "") 30 | , _colLabel(n, "") 31 | , _labelsSet(false) 32 | { 33 | } 34 | 35 | void Matrix::setRowLabels(const std::string& labels) 36 | { 37 | _labelsSet = true; 38 | std::stringstream ss(labels); 39 | for (int i = 0; i < _m; ++i) 40 | { 41 | ss >> _rowLabel[i]; 42 | } 43 | } 44 | 45 | void Matrix::setColLabels(const std::string& labels) 46 | { 47 | typedef std::vector StringVector; 48 | 49 | _labelsSet = true; 50 | 51 | StringVector s; 52 | boost::split(s, labels, boost::is_any_of(" ")); 53 | 54 | assert(s.size() >= _n); 55 | 56 | std::stringstream ss(labels); 57 | for (int j = 0; j < _n; ++j) 58 | { 59 | _colLabel[j] = s[j]; 60 | } 61 | } 62 | 63 | void Matrix::setLabels(std::istream& in) 64 | { 65 | _labelsSet = true; 66 | std::string line; 67 | vaff::getline(in, line); 68 | 69 | vaff::getline(in, line); 70 | setRowLabels(line); 71 | 72 | vaff::getline(in, line); 73 | setColLabels(line); 74 | } 75 | 76 | } // namespace vaff 77 | -------------------------------------------------------------------------------- /src/probcomparison.h: -------------------------------------------------------------------------------- 1 | /* 2 | * probcomparison.h 3 | * 4 | * Created on: 26-mar-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef PROBCOMPARISON_H 9 | #define PROBCOMPARISON_H 10 | 11 | #include "utils.h" 12 | #include "maxsolution.h" 13 | #include "clonaltree.h" 14 | 15 | #include 16 | #include 17 | 18 | namespace vaff { 19 | 20 | class ProbComparison 21 | { 22 | public: 23 | ProbComparison(const AncestryMatrix& A, 24 | const MaxSolution::Triple& solution); 25 | 26 | StlDoubleVector clustered() const; 27 | StlDoubleVector ancestral() const; 28 | StlDoubleVector incomparable() const; 29 | 30 | static double median(StlDoubleVector& S) 31 | { 32 | if (S.size() % 2 == 1) 33 | { 34 | std::nth_element(S.begin(), S.begin() + S.size() / 2, S.end()); 35 | return S[S.size() / 2]; 36 | } 37 | else 38 | { 39 | std::nth_element(S.begin(), S.begin() + S.size() / 2 - 1, S.end()); 40 | std::nth_element(S.begin(), S.begin() + S.size() / 2, S.end()); 41 | 42 | return (S[S.size() / 2] + S[S.size() / 2 - 1]) / 2; 43 | } 44 | } 45 | 46 | private: 47 | typedef std::pair StlIntPair; 48 | typedef std::set StlIntPairSet; 49 | 50 | const AncestryMatrix& _A; 51 | const MaxSolution::Triple& _solution; 52 | StlIntMatrix _toMutationsFromSol; 53 | StlIntVector _toSolCluster; 54 | StlIntPairSet _clustered; 55 | StlIntPairSet _ancestral; 56 | StlIntPairSet _incomparable; 57 | 58 | void constructMappings(); 59 | 60 | void determinePairs(); 61 | }; 62 | 63 | } // namespace vaff 64 | 65 | #endif // PROBCOMPARISON_H 66 | -------------------------------------------------------------------------------- /src/realintervalmatrix.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * realintervalmatrix.cpp 3 | * 4 | * Created on: 7-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "realintervalmatrix.h" 9 | 10 | namespace vaff { 11 | 12 | RealIntervalMatrix::RealIntervalMatrix() 13 | : Matrix() 14 | , _C() 15 | { 16 | } 17 | 18 | RealIntervalMatrix::RealIntervalMatrix(int m, int n) 19 | : Matrix(m, n) 20 | , _C(m, StlRealIntervalVector(n)) 21 | { 22 | } 23 | 24 | void RealIntervalMatrix::obtainPointEstimates(RealMatrix& F) const 25 | { 26 | F = RealMatrix(_m, _n); 27 | for (int i = 0; i < _m; ++i) 28 | { 29 | for (int j = 0; j < _n; ++j) 30 | { 31 | const RealInterval& interval = _C[i][j]; 32 | F.set(i, j, 0.5 * (interval.first + interval.second)); 33 | } 34 | } 35 | } 36 | 37 | std::ostream& operator<<(std::ostream& out, 38 | const RealIntervalMatrix& matrix) 39 | { 40 | out << matrix._C; 41 | if (matrix._labelsSet) 42 | { 43 | out << std::endl; 44 | 45 | for (int i = 0; i < matrix._m; ++i) 46 | { 47 | out << matrix._rowLabel[i] << " "; 48 | } 49 | out << std::endl; 50 | 51 | for (int j = 0; j < matrix._n; ++j) 52 | { 53 | out << matrix._colLabel[j] << " "; 54 | } 55 | out << std::endl; 56 | } 57 | return out; 58 | } 59 | 60 | std::istream& operator>>(std::istream& in, 61 | RealIntervalMatrix& matrix) 62 | { 63 | in >> matrix._C; 64 | 65 | matrix._m = matrix._C.size(); 66 | matrix._n = matrix._C.empty() ? 0 : matrix._C.front().size(); 67 | matrix._rowLabel.resize(matrix._m); 68 | matrix._colLabel.resize(matrix._n); 69 | 70 | return in; 71 | } 72 | 73 | } // namespace vaff 74 | -------------------------------------------------------------------------------- /data/real/283_whole.txt: -------------------------------------------------------------------------------- 1 | gene_id 12 12 14 14 15 15 17 17 18 18 2 | LONRF2,2.0,100911933 192 61 171 23 146 21 139 26 161 29 3 | CACNA1F,X,49072908 104 14 4 | TUBD1,17.0,57941133 269 26 172 15 188 18 188 14 187 19 5 | PDCD11,10.0,105160144 190 47 101 19 139 25 114 19 112 23 6 | ADAM21P1,14.0,70713759 467 56 322 22 423 37 363 27 349 21 7 | NRXN1,2.0,51254673 201 27 108 9 180 11 139 17 133 23 8 | PPM1D,17.0,58678223 194 17 153 21 199 27 183 21 183 13 9 | SNX4,3.0,125223414 148 13 116 8 152 11 106 6 147 17 10 | RPTOR,17.0,78867449 114 54 50 32 61 26 55 28 58 20 11 | LOC642236,9.0,68452937 232 16 136 8 175 6 229 20 187 20 12 | ARAP3,5.0,141059682 228 32 208 22 222 9 210 20 222 18 13 | FAM171A1,10.0,15290777 135 13 116 0 151 2 106 3 14 | ITSN1,21.0,35127600 234 15 154 17 185 12 185 13 180 17 15 | COL6A2,21.0,47537279 116 14 96 12 143 18 129 12 114 7 16 | RGS6,14.0,72457699 132 18 103 7 92 10 96 20 74 4 17 | ZNF646,16.0,31094270 302 28 240 6 281 15 282 16 296 10 18 | PCNXL2,1.0,233388288 182 80 106 24 138 41 125 32 150 41 19 | PPP1R16A,8.0,145725585 177 36 80 17 116 15 113 31 120 18 20 | CATSPERG,19.0,38853266 233 46 173 34 240 36 182 30 203 39 21 | SOX5,12.0,23696151 243 53 161 39 168 24 169 48 181 47 22 | DENND5B,12.0,31605136 429 34 312 20 350 21 330 28 304 37 23 | DSE,6.0,116758326 158 11 138 14 155 16 123 7 140 9 24 | PPFIA1,11.0,70194462 503 53 312 23 382 27 426 44 417 30 25 | JA660597(dist=291601),UBE2MP1(dist=146667),16.0,34257135 249 26 176 15 214 21 214 18 188 15 26 | NTSR2,2.0,11802268 219 15 174 15 182 19 163 15 154 10 27 | BTBD1,15.0,83687467 330 71 227 38 228 37 234 36 249 45 28 | EFNA2,19.0,1295565 253 15 246 4 29 | NONE(dist=NONE),ANKRD26P1(dist=100642),16.0,46402607 23 0 29 0 63 0 36 1 30 | FBXO2,1.0,11709981 186 61 155 40 177 29 160 46 169 35 31 | -------------------------------------------------------------------------------- /src/matrix.h: -------------------------------------------------------------------------------- 1 | /* 2 | * matrix.h 3 | * 4 | * Created on: 22-dec-2014 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef MATRIX_H 9 | #define MATRIX_H 10 | 11 | #include 12 | #include 13 | #include 14 | 15 | namespace vaff { 16 | 17 | class Matrix 18 | { 19 | public: 20 | typedef std::vector StringVector; 21 | 22 | Matrix(); 23 | 24 | Matrix(int m, int n); 25 | 26 | int getNrRows() const 27 | { 28 | return _m; 29 | } 30 | 31 | int getNrCols() const 32 | { 33 | return _n; 34 | } 35 | 36 | void setLabels(std::istream& in); 37 | 38 | const std::string& getRowLabel(int i) const 39 | { 40 | assert(0 <= i && i < _m); 41 | return _rowLabel[i]; 42 | } 43 | 44 | const StringVector& getRowLabels() const 45 | { 46 | return _rowLabel; 47 | } 48 | 49 | const StringVector& getColLabels() const 50 | { 51 | return _colLabel; 52 | } 53 | 54 | const std::string& getColLabel(int j) const 55 | { 56 | assert(0 <= j && j < _n); 57 | return _colLabel[j]; 58 | } 59 | 60 | void setRowLabel(int i, const std::string& label) 61 | { 62 | assert(0 <= i && i < _m); 63 | _rowLabel[i] = label; 64 | _labelsSet = true; 65 | } 66 | 67 | void setColLabel(int j, const std::string& label) 68 | { 69 | assert(0 <= j && j < _n); 70 | _colLabel[j] = label; 71 | _labelsSet = true; 72 | } 73 | 74 | protected: 75 | int _m; 76 | int _n; 77 | StringVector _rowLabel; 78 | StringVector _colLabel; 79 | bool _labelsSet; 80 | 81 | private: 82 | void setRowLabels(const std::string& labels); 83 | void setColLabels(const std::string& labels); 84 | }; 85 | 86 | } // namespace vaff 87 | 88 | #endif // MATRIX_H -------------------------------------------------------------------------------- /src/realmatrix.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * realmatrix.cpp 3 | * 4 | * Created on: 22-dec-2014 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "realmatrix.h" 9 | 10 | namespace vaff { 11 | 12 | RealMatrix::RealMatrix() 13 | : Matrix() 14 | , _C() 15 | { 16 | } 17 | 18 | RealMatrix::RealMatrix(int m, int n) 19 | : Matrix(m, n) 20 | , _C(m, StlDoubleVector(n, 0)) 21 | { 22 | } 23 | 24 | std::ostream& operator<<(std::ostream& out, 25 | const RealMatrix& matrix) 26 | { 27 | out << matrix._C; 28 | if (matrix._labelsSet) 29 | { 30 | out << std::endl; 31 | 32 | for (int i = 0; i < matrix._m; ++i) 33 | { 34 | out << matrix._rowLabel[i] << " "; 35 | } 36 | out << std::endl; 37 | 38 | for (int j = 0; j < matrix._n; ++j) 39 | { 40 | out << matrix._colLabel[j] << " "; 41 | } 42 | out << std::endl; 43 | } 44 | return out; 45 | } 46 | 47 | std::istream& operator>>(std::istream& in, 48 | RealMatrix& matrix) 49 | { 50 | in >> matrix._C; 51 | 52 | matrix._m = matrix._C.size(); 53 | matrix._n = matrix._C.empty() ? 0 : matrix._C.front().size(); 54 | matrix._rowLabel.resize(matrix._m); 55 | matrix._colLabel.resize(matrix._n); 56 | 57 | return in; 58 | } 59 | 60 | RealMatrix RealMatrix::subMatrix(const StlIntVector& columns) const 61 | { 62 | int n = columns.size(); 63 | 64 | RealMatrix res(_m, n); 65 | res._rowLabel = _rowLabel; 66 | 67 | for (int j = 0; j < n; ++j) 68 | { 69 | int jj = columns[j]; 70 | res._colLabel[j] = _colLabel[jj]; 71 | for (int i = 0; i < _m; ++i) 72 | { 73 | res._C[i][j] = _C[i][jj]; 74 | } 75 | } 76 | 77 | res._labelsSet = _labelsSet; 78 | 79 | return res; 80 | } 81 | 82 | } // namespace vaff 83 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | Copyright 2015, 2016 and 2017, Brown University, Providence, RI. 2 | 3 | All Rights Reserved 4 | 5 | Permission to use this software, and any documentation, for non-commercial academic research purposes only is hereby granted with the following terms and conditions: 6 | (1) the above copyright notice and this permission notice shall be preserved in all instances of the software and in any supporting documentation; 7 | (2) the name of Brown University shall not be used in advertising or publicity pertaining to the use of the software without specific, written prior permission; 8 | (3) the rights granted herein are individual and personal to the recipient and may not be sublicensed or distributed to any third party without specific, written prior permission; and 9 | (4) the permitted user acknowledges that all commercial rights are licensed to Medley Genomics, Inc., and any inquiries related to commercial use shall be directed to Medley Genomics, Inc. 10 | 11 | BROWN UNIVERSITY PROVIDES THIS SOFTWARE AND ANY DOCUMENTATION “AS IS” AND DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE AND ANY DOCUMENTATION, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR ANY PARTICULAR PURPOSE. IN NO EVENT SHALL BROWN UNIVERSITY BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER ACTION BASED ON ANY OTHER LEGAL THEORY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. 12 | 13 | REFERENCES: 14 | 15 | If you use our code in your research, please cite: 16 | 17 | M. El-Kebir, L. Oesper, H. Acheson-Field, and B.J. Raphael. 18 | (2015) Reconstruction of clonal trees and tumor composition from 19 | multi-sample cancer sequencing data. Bioninformatics. 20 | -------------------------------------------------------------------------------- /src/utils.h: -------------------------------------------------------------------------------- 1 | /* 2 | * utils.h 3 | * 4 | * Created on: 22-dec-2014 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef UTILS_H 9 | #define UTILS_H 10 | 11 | #include 12 | #include 13 | #include 14 | #include 15 | #include 16 | #include 17 | #include 18 | #include 19 | #include 20 | #include 21 | #include 22 | #include 23 | 24 | namespace vaff { 25 | 26 | typedef std::vector StlBoolVector; 27 | typedef std::vector StlBoolMatrix; 28 | 29 | typedef std::vector StlIntVector; 30 | typedef StlIntVector::const_iterator StlIntVectorIt; 31 | typedef std::vector StlIntMatrix; 32 | typedef StlIntMatrix::const_iterator StlIntMatrixIt; 33 | 34 | typedef std::vector StlDoubleVector; 35 | typedef std::vector StlDoubleMatrix; 36 | 37 | typedef std::pair RealInterval; 38 | typedef std::vector StlRealIntervalVector; 39 | typedef std::vector StlRealIntervalMatrix; 40 | 41 | typedef std::pair IntPair; 42 | 43 | std::ostream& operator<<(std::ostream& out, const StlBoolMatrix& M); 44 | std::istream& operator>>(std::istream& in, StlBoolMatrix& M); 45 | 46 | std::ostream& operator<<(std::ostream& out, const StlDoubleMatrix& M); 47 | std::istream& operator>>(std::istream& in, StlDoubleMatrix& M); 48 | 49 | std::ostream& operator<<(std::ostream& out, const StlRealIntervalMatrix& M); 50 | std::istream& operator>>(std::istream& in, StlRealIntervalMatrix& M); 51 | 52 | StlBoolVector discretize(const StlDoubleVector& v); 53 | 54 | StlBoolMatrix discretize(const StlDoubleMatrix& M); 55 | 56 | std::istream& getline(std::istream& is, std::string& t); 57 | 58 | extern lemon::Tolerance g_tol; 59 | 60 | } // namespace vaff 61 | 62 | #endif // UTILS_H 63 | -------------------------------------------------------------------------------- /src/machinainput.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * machinainput.cpp 3 | * 4 | * Created on: 30-nov-2017 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "utils.h" 9 | #include "maxsolution.h" 10 | #include "solutiongraph.h" 11 | #include 12 | #include 13 | 14 | using namespace vaff; 15 | 16 | void printUsage(const char* argv0, std::ostream& out) 17 | { 18 | out << "Usage: " << argv0 << " where" << std::endl 19 | << " is the solution index" << std::endl 20 | << " is the solution file, specify '-' to use stdin" << std::endl 21 | << " usage threshold" << std::endl 22 | << " beta" << std::endl; 23 | } 24 | 25 | 26 | int main(int argc, char** argv) 27 | { 28 | if (argc != 5) 29 | { 30 | printUsage(argv[0], std::cerr); 31 | return 1; 32 | } 33 | 34 | int sol_idx = atoi(argv[1]); 35 | std::string filename = argv[2]; 36 | 37 | double threshold = -1; 38 | sscanf(argv[3], "%lf", &threshold); 39 | if (!(0 <= threshold && threshold <= 1.0)) 40 | { 41 | std::cerr << "Error: threshold must be in [0,1.0]" << std::endl; 42 | return 1; 43 | } 44 | 45 | double beta = -1; 46 | sscanf(argv[4], "%lf", &beta); 47 | if (!(0.5 <= beta && beta <= 1)) 48 | { 49 | std::cerr << "Error: beta must be in [0.5,1]" << std::endl; 50 | return 1; 51 | } 52 | 53 | MaxSolution solution; 54 | 55 | if (filename != "-") 56 | { 57 | std::ifstream in(filename.c_str()); 58 | if (!in.good()) 59 | { 60 | std::cerr << "Error: failed to open '" << argv[2] << "' for reading" << std::endl; 61 | return 1; 62 | } 63 | in >> solution; 64 | in.close(); 65 | } 66 | else 67 | { 68 | std::cin >> solution; 69 | } 70 | 71 | solution.remapLabels(-1); 72 | SolutionGraph graph(solution.solution(sol_idx), threshold, beta); 73 | graph.writeEdgeList(std::cout); 74 | graph.writeLeaves(std::cerr); 75 | 76 | return 0; 77 | } 78 | -------------------------------------------------------------------------------- /data/real/283_deep.txt: -------------------------------------------------------------------------------- 1 | gene_id 12 12 14 14 15 15 17 17 18 18 2 | LONRF2,2.0,100911933 683 137 575 99 609 88 651 113 628 109 3 | CACNA1F,X,49072908 194 9 4 | TUBD1,17.0,57941133 634 64 583 43 596 33 600 42 577 44 5 | PDCD11,10.0,105160144 381 84 326 61 363 68 338 52 326 49 6 | ADAM21P1,14.0,70713759 862 55 893 63 895 44 864 55 877 46 7 | NRXN1,2.0,51254673 787 127 850 69 858 73 840 96 852 68 8 | PPM1D,17.0,58678223 734 68 610 68 688 49 670 45 641 67 9 | SNX4,3.0,125223414 541 60 490 41 463 35 476 35 498 49 10 | RPTOR,17.0,78867449 319 137 274 92 292 59 248 102 238 115 11 | LOC642236,9.0,68452937 565 57 442 39 497 29 425 51 508 28 12 | ARAP3,5.0,141059682 418 55 385 23 348 26 334 23 381 23 13 | FAM171A1,10.0,15290777 404 27 390 7 364 11 368 4 14 | ITSN1(uc002ysx.3:exon8:c.513-2A>G,uc002ysz.3:exon8:c.624-2A>G,uc010gmg.3:exon8:c.513-2A>G,uc002ysw.3:exon8:c.624-2A>G,uc010gmi.3:exon8:c.513-2A>G,uc010gmj.3:exon7:c.276-2A>G,uc002ysy.3:exon8:c.624-2A>G,uc002yta.1:exon8:c.624-2A>G,uc002ytb.1:exon8:c.624-2A>G,uc002ytc.1:exon7:c.624-2A>G,uc010gmk.3:exon7:c.513-2A>G,uc002ytj.2:exon7:c.624-2A>G,uc002yte.3:exon5:c.426-2A>G,uc021wip.1:exon3:c.306-2A>G),21.0,35127600 595 41 534 42 520 21 497 31 546 30 15 | COL6A2,21.0,47537279 819 83 695 65 739 52 749 79 719 59 16 | RGS6,14.0,72457699 814 104 677 69 791 49 778 65 773 62 17 | ZNF646,16.0,31094270 843 83 807 55 819 26 797 52 812 52 18 | PCNXL2,1.0,233388288 273 91 237 43 243 55 256 41 196 47 19 | PPP1R16A,8.0,145725585 594 138 471 114 572 90 491 123 469 84 20 | CATSPERG,19.0,38853266 116 19 116 13 104 17 106 20 107 16 21 | SOX5,12.0,23696151 722 163 614 123 664 130 594 148 611 109 22 | DENND5B,12.0,31605136 819 96 820 70 824 86 816 70 852 64 23 | DSE,6.0,116758326 615 66 578 45 630 48 580 44 606 44 24 | PPFIA1,11.0,70194462 879 69 836 59 827 48 854 78 823 62 25 | JA660597(dist=291601),UBE2MP1(dist=146667),16.0,34257135 868 74 853 54 860 47 852 70 863 68 26 | NTSR2,2.0,11802268 440 40 407 34 376 29 370 35 357 46 27 | BTBD1,15.0,83687467 735 156 704 143 782 116 705 121 702 111 28 | EFNA2,19.0,1295565 496 20 356 5 29 | NONE(dist=NONE),ANKRD26P1(dist=100642),16.0,46402607 416 12 392 4 397 6 446 5 30 | FBXO2,1.0,11709981 608 169 524 169 598 109 507 136 557 136 31 | -------------------------------------------------------------------------------- /src/visualizesolution.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * visualizesolution.cpp 3 | * 4 | * Created on: 4-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "utils.h" 9 | #include "maxsolution.h" 10 | #include "solutiongraph.h" 11 | #include 12 | #include 13 | 14 | using namespace vaff; 15 | 16 | void printUsage(const char* argv0, std::ostream& out) 17 | { 18 | out << "Usage: " << argv0 << " where" << std::endl 19 | << " is the solution index" << std::endl 20 | << " is the solution file, specify '-' to use stdin" << std::endl 21 | << " usage threshold" << std::endl 22 | << " max cluster size" << std::endl 23 | << " beta" << std::endl; 24 | } 25 | 26 | int main(int argc, char** argv) 27 | { 28 | if (argc != 6) 29 | { 30 | printUsage(argv[0], std::cerr); 31 | return 1; 32 | } 33 | 34 | int sol_idx = atoi(argv[1]); 35 | std::string filename = argv[2]; 36 | 37 | double threshold = -1; 38 | sscanf(argv[3], "%lf", &threshold); 39 | if (!(0 <= threshold && threshold <= 1.0)) 40 | { 41 | std::cerr << "Error: threshold must be in [0,1.0]" << std::endl; 42 | return 1; 43 | } 44 | 45 | int max_cluster_size = atoi(argv[4]); 46 | 47 | double beta = -1; 48 | sscanf(argv[5], "%lf", &beta); 49 | if (!(0.5 <= beta && beta <= 1)) 50 | { 51 | std::cerr << "Error: beta must be in [0.5,1]" << std::endl; 52 | return 1; 53 | } 54 | 55 | MaxSolution solution; 56 | 57 | if (filename != "-") 58 | { 59 | std::ifstream in(filename.c_str()); 60 | if (!in.good()) 61 | { 62 | std::cerr << "Error: failed to open '" << filename << "' for reading" << std::endl; 63 | return 1; 64 | } 65 | in >> solution; 66 | in.close(); 67 | } 68 | else 69 | { 70 | std::cin >> solution; 71 | } 72 | 73 | if (!(0 <= sol_idx && sol_idx < solution.size())) 74 | { 75 | std::cerr << "Invalid solution index " << sol_idx << "; it must be in the range [0, " << solution.size() << ")" << std::endl; 76 | return 1; 77 | } 78 | 79 | solution.remapLabels(max_cluster_size); 80 | SolutionGraph graph(solution.solution(sol_idx), threshold, beta); 81 | graph.writeDOT(std::cout); 82 | 83 | return 0; 84 | } 85 | -------------------------------------------------------------------------------- /src/comparison.h: -------------------------------------------------------------------------------- 1 | /* 2 | * comparison.h 3 | * 4 | * Created on: 12-mar-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef COMPARISON_H 9 | #define COMPARISON_H 10 | 11 | #include "utils.h" 12 | #include "maxsolution.h" 13 | #include "clonaltree.h" 14 | 15 | #include 16 | #include 17 | 18 | namespace vaff { 19 | 20 | class Comparison 21 | { 22 | public: 23 | Comparison(const MaxSolution& referenceSolution, 24 | const MaxSolution::Triple& solution, 25 | const MaxSolution::Triple& whitelistSolution); 26 | 27 | double coverage() const; 28 | 29 | double deltaF() const; 30 | 31 | double deltaU() const; 32 | 33 | void accuracyB(double& clustered, 34 | double& ancestral, 35 | double& incomparable) const; 36 | 37 | void recallB(double& clustered, 38 | double& ancestral, 39 | double& incomparable) const; 40 | 41 | private: 42 | typedef std::pair StlIntPair; 43 | typedef std::set StlIntSet; 44 | 45 | const MaxSolution& _referenceSolution; 46 | const MaxSolution::Triple& _solution; 47 | StlIntMatrix _toMutationsFromSol; 48 | StlIntMatrix _toMutationsFromRef; 49 | StlIntVector _toSolCluster; 50 | StlIntVector _toRefCluster; 51 | StlBoolVector _whitelist; 52 | 53 | void constructMappings(const MaxSolution::Triple& whitelistSolution); 54 | 55 | void determinePairs(const MaxSolution::Triple& solution, 56 | const StlIntMatrix& toMutations, 57 | const StlIntVector& toCluster, 58 | StlIntSet& P_clustered, 59 | StlIntSet& N_clustered, 60 | StlIntSet& P_ancestral, 61 | StlIntSet& N_ancestral, 62 | StlIntSet& P_incomparable, 63 | StlIntSet& N_incomparable) const; 64 | 65 | void determineNodeMapping(StlIntVector& ref2sol, 66 | StlIntVector& sol2ref) const; 67 | 68 | double recall(const StlIntSet& S_ref, 69 | const StlIntSet& S_sol) const; 70 | 71 | double accuracy(const StlIntSet& P_ref, 72 | const StlIntSet& N_ref, 73 | const StlIntSet& P_sol, 74 | const StlIntSet& N_sol) const; 75 | }; 76 | 77 | } // namespace vaff 78 | 79 | #endif // COMPARISON_H 80 | -------------------------------------------------------------------------------- /src/cluster.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * analyse.cpp 3 | * 4 | * Created on: 10-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "utils.h" 9 | #include "ancestrymatrix.h" 10 | #include "readcountmatrix.h" 11 | //#include "probancestrygraphyoshiko.h" 12 | #include "probancestrygraph.h" 13 | #include 14 | 15 | #include 16 | 17 | using namespace vaff; 18 | 19 | void printUsage(const char* argv0, std::ostream& out) 20 | { 21 | out << "Usage: " << argv0 << " where" << std::endl 22 | << " is the ancestry matrix file" << std::endl 23 | << " alpha parameter (ancestry)" << std::endl 24 | << " beta parameter (equality)" << std::endl 25 | << " gamma parameter (CI)" << std::endl; 26 | } 27 | 28 | int main(int argc, char** argv) 29 | { 30 | if (argc != 5) 31 | { 32 | printUsage(argv[0], std::cerr); 33 | return 1; 34 | } 35 | 36 | double alpha = -1; 37 | sscanf(argv[2], "%lf", &alpha); 38 | if (!(0 <= alpha && alpha <= 0.5)) 39 | { 40 | std::cerr << "Error: alpha must be in [0,0.5]" << std::endl; 41 | return 1; 42 | } 43 | 44 | double beta = -1; 45 | sscanf(argv[3], "%lf", &beta); 46 | if (!(0.5 <= beta && beta <= 1)) 47 | { 48 | std::cerr << "Error: beta must be in [0.5,1]" << std::endl; 49 | return 1; 50 | } 51 | 52 | double gamma = -1; 53 | sscanf(argv[4], "%lf", &gamma); 54 | if (!(0 <= gamma && gamma <= 1)) 55 | { 56 | std::cerr << "Error: gamma must be in [0,1]" << std::endl; 57 | return 1; 58 | } 59 | 60 | ReadCountMatrix R; 61 | std::string read_count_matrix = argv[1]; 62 | 63 | if (read_count_matrix != "-") 64 | { 65 | std::ifstream in(read_count_matrix.c_str()); 66 | if (!in.good()) 67 | { 68 | std::cerr << "Error: failed to open '" << read_count_matrix << "' for reading" << std::endl; 69 | return 1; 70 | } 71 | in >> R; 72 | in.close(); 73 | } 74 | else 75 | { 76 | std::cin >> R; 77 | } 78 | 79 | AncestryMatrix A(R, 0); 80 | 81 | ProbAncestryGraph G(A, R, alpha, gamma); 82 | 83 | StlIntMatrix toOrginalColumns; 84 | G.removeCycles(A, alpha, toOrginalColumns); 85 | 86 | ReadCountMatrix newR = R.collapse(toOrginalColumns); 87 | newR.remapLabels(toOrginalColumns, R); 88 | RealIntervalMatrix CI; 89 | newR.computeConfidenceIntervals(CI, gamma); 90 | 91 | ProbAncestryGraph H; 92 | G.contract(A, toOrginalColumns, beta, H); 93 | 94 | std::cout << CI; 95 | std::cout << newR; 96 | 97 | return 0; 98 | } -------------------------------------------------------------------------------- /src/solutiongraph.h: -------------------------------------------------------------------------------- 1 | /* 2 | * solutiongraph.h 3 | * 4 | * Created on: 4-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef SOLUTIONGRAPH_H 9 | #define SOLUTIONGRAPH_H 10 | 11 | #include 12 | #include 13 | #include "utils.h" 14 | #include "realmatrix.h" 15 | #include "maxsolution.h" 16 | #include "clonaltree.h" 17 | 18 | namespace vaff { 19 | 20 | class SolutionGraph 21 | { 22 | public: 23 | typedef lemon::ListBpGraph MixingGraph; 24 | typedef ClonalTree::Tree Tree; 25 | DIGRAPH_TYPEDEFS(ClonalTree::Tree); 26 | typedef MixingGraph::Node BpNode; 27 | typedef MixingGraph::NodeIt BpNodeIt; 28 | typedef MixingGraph::BlueNode BpBlueNode; 29 | typedef MixingGraph::BlueNodeIt BpBlueNodeIt; 30 | typedef MixingGraph::RedNode BpRedNode; 31 | typedef MixingGraph::RedNodeIt BpRedNodeIt; 32 | typedef MixingGraph::Edge BpEdge; 33 | typedef MixingGraph::EdgeIt BpEdgeIt; 34 | typedef MixingGraph::RedNodeMap IntBpRedNodeMap; 35 | typedef MixingGraph::BlueNodeMap IntBpBlueNodeMap; 36 | typedef MixingGraph::NodeMap BoolVectorBpNodeMap; 37 | 38 | SolutionGraph(const MaxSolution::Triple& sol, 39 | double threshold, 40 | double beta); 41 | 42 | void writeDOT(std::ostream& out) const; 43 | 44 | const MixingGraph& getMixingGraph() const 45 | { 46 | return _G; 47 | } 48 | 49 | void writeEdgeList(std::ostream& out) const; 50 | 51 | void writeLeaves(std::ostream& out) const; 52 | 53 | private: 54 | typedef std::vector NodeVector; 55 | typedef Tree::NodeMap BoolVectorNodeMap; 56 | typedef Tree::NodeMap BpBlueNodeNodeMap; 57 | 58 | typedef std::vector BpRedNodeVector; 59 | typedef std::vector BpBlueNodeVector; 60 | typedef MixingGraph::RedNodeMap BoolVectorRedNodeMap; 61 | typedef MixingGraph::BlueNodeMap NodeBpBlueNodeMap; 62 | typedef MixingGraph::EdgeMap MixingEdgeMap; 63 | 64 | const MaxSolution::Triple& _sol; 65 | 66 | BpBlueNodeNodeMap _toMixingGraph; 67 | BoolNodeMap _leaf; 68 | 69 | // red node: samples 70 | // blue node: deconvoluted samples 71 | lemon::ListBpGraph _G; 72 | IntBpRedNodeMap _bpNodeToRow; 73 | BpRedNodeVector _rowToBpNode; 74 | IntBpBlueNodeMap _bpNodeToBasisRow; 75 | BoolVectorBpNodeMap _mixingLabel; 76 | MixingEdgeMap _mixingFraction; 77 | NodeBpBlueNodeMap _toTree; 78 | double _threshold; 79 | double _beta; 80 | 81 | void constructMixingGraph(); 82 | }; 83 | 84 | 85 | } // namespace vaff 86 | 87 | #endif // SOLUTIONGRAPH_H 88 | -------------------------------------------------------------------------------- /src/intmaxilpsolver.h: -------------------------------------------------------------------------------- 1 | /* 2 | * intmaxilpsolver.h 3 | * 4 | * Created on: 8-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef INTMAXILPSOLVER_H 9 | #define INTMAXILPSOLVER_H 10 | 11 | #include 12 | #include "baseancestrygraph.h" 13 | #include "realintervalmatrix.h" 14 | #include "maxsolution.h" 15 | #include 16 | 17 | namespace vaff { 18 | 19 | class IntMaxIlpSolver 20 | { 21 | public: 22 | IntMaxIlpSolver(const BaseAncestryGraph& G, 23 | const RealIntervalMatrix& F_interval_clustered, 24 | const RealMatrix& F_point_unclustered, 25 | const StlIntMatrix& toUnclusteredColumn, 26 | int timeLimit); 27 | 28 | ~IntMaxIlpSolver(); 29 | 30 | bool solve(MaxSolution& solution); 31 | 32 | void exportModel(const std::string& filename) 33 | { 34 | _cplex.exportModel(filename.c_str()); 35 | } 36 | 37 | protected: 38 | typedef BaseAncestryGraph::Digraph Digraph; 39 | DIGRAPH_TYPEDEFS(Digraph); 40 | 41 | typedef std::vector ArcVector; 42 | typedef std::vector NodeVector; 43 | 44 | void initVariables(); 45 | void initConstraints(); 46 | void initObjective(); 47 | 48 | void printVariables(int solIdx, std::ostream& out) const; 49 | 50 | void processSolution(int solIdx, MaxSolution::Triple& sol) const; 51 | 52 | typedef IloArray IloBoolVarMatrix; 53 | typedef IloArray IloBoolMatrix; 54 | typedef IloArray IloBoolVar3Matrix; 55 | 56 | typedef IloArray IloNumVarMatrix; 57 | typedef IloArray IloNumMatrix; 58 | typedef IloArray IloNumVar3Matrix; 59 | 60 | const BaseAncestryGraph& _G; 61 | const RealIntervalMatrix& _F_interval_clustered; 62 | const RealMatrix& _F_point_unclustered; 63 | const StlIntMatrix& _toUnclusteredColumn; 64 | const int _timeLimit; 65 | 66 | const int _nodeCount; 67 | const IntNodeMap& _nodeToIndex; 68 | const NodeVector& _indexToNode; 69 | IntNodeMap _nodeToRootArcIndex; 70 | 71 | const int _arcCount; 72 | IntArcMap _arcToIndex; 73 | ArcVector _indexToArc; 74 | 75 | IloEnv _env; 76 | IloModel _model; 77 | IloCplex _cplex; 78 | 79 | // x[(j,k)] : arc (v_j,v_k) is in the solution 80 | IloBoolVarArray _x; 81 | // f[i][j] : corrected VAF for sample i and mutation j 82 | IloNumVarMatrix _f; 83 | // fx[i][j][(k,l)] = f[i][j] * x[(k,l)] 84 | IloNumVar3Matrix _fx; 85 | // f[i][j] : VAF deviation for sample i and unclustered mutation j 86 | IloNumVarMatrix _g; 87 | }; 88 | 89 | } 90 | 91 | #endif // MAXILPSOLVER_H -------------------------------------------------------------------------------- /doc/CLL077_whole.dot: -------------------------------------------------------------------------------- 1 | graph G { 2 | subgraph mixed { 3 | s4 [colorscheme=paired10,penwidth=5,fontsize=60,color=5,shape=box,label="e"] 4 | s3 [colorscheme=paired10,penwidth=5,fontsize=60,color=4,shape=box,label="d"] 5 | s2 [colorscheme=paired10,penwidth=5,fontsize=60,color=3,shape=box,label="c"] 6 | s1 [colorscheme=paired10,penwidth=5,fontsize=60,color=2,shape=box,label="b"] 7 | s0 [colorscheme=paired10,penwidth=5,fontsize=60,color=1,shape=box,label="a"] 8 | } 9 | subgraph unmixed { 10 | subgraph 0 { 11 | rank=same 12 | 4 [penwidth=5,fontsize=35,label="IRF2BP2 13 | GPR158"] 14 | } 15 | subgraph leaves { 16 | rank=same 17 | 3 [penwidth=5,fontsize=35,label="LRRC16A"] 18 | 2 [penwidth=5,fontsize=35,label="DDX1"] 19 | 1 [penwidth=5,fontsize=35,label="ZFHX4 20 | NOD1 21 | KLHDC2 22 | HMCN1 23 | COL24A1"] 24 | 0 [penwidth=5,fontsize=35,label="ZNF566"] 25 | dup0 [penwidth=5,fontsize=35,label="IRF2BP2 26 | GPR158"] 27 | } 28 | } 29 | 4 -- 1 [penwidth=9.546516,fontsize=35,label=" 0.98"] 30 | 4 -- 2 [penwidth=9.47,fontsize=35,label=" 0.98"] 31 | 4 -- 3 [penwidth=8.41,fontsize=35,label=" 0.94"] 32 | 4 -- 0 [penwidth=9.71,fontsize=35,label=" 0.99"] 33 | 1 -- s4 [splines=none,colorscheme=paired10,color=5,minlen=4,fontsize=35,label=0.36,penwidth=13.97] 34 | 2 -- s4 [splines=none,colorscheme=paired10,color=5,minlen=4,fontsize=35,label=0.24,penwidth=10.99] 35 | 0 -- s4 [splines=none,colorscheme=paired10,color=5,minlen=4,fontsize=35,label=0.11,penwidth=7.81] 36 | 1 -- s3 [splines=none,colorscheme=paired10,color=4,minlen=4,fontsize=35,label=0.18,penwidth=9.55] 37 | 2 -- s3 [splines=none,colorscheme=paired10,color=4,minlen=4,fontsize=35,label=0.14,penwidth=8.45] 38 | 3 -- s3 [splines=none,colorscheme=paired10,color=4,minlen=4,fontsize=35,label=0.34,penwidth=13.54] 39 | dup0 -- s3 [splines=none,colorscheme=paired10,color=4,minlen=4,fontsize=35,label=0.14,penwidth=8.47] 40 | 2 -- s2 [splines=none,colorscheme=paired10,color=3,minlen=4,fontsize=35,label=0.19,penwidth=9.65] 41 | 3 -- s2 [splines=none,colorscheme=paired10,color=3,minlen=4,fontsize=35,label=0.27,penwidth=11.67] 42 | dup0 -- s2 [splines=none,colorscheme=paired10,color=3,minlen=4,fontsize=35,label=0.55,penwidth=18.66] 43 | 3 -- s1 [splines=none,colorscheme=paired10,color=2,minlen=4,fontsize=35,label=0.52,penwidth=17.90] 44 | dup0 -- s1 [splines=none,colorscheme=paired10,color=2,minlen=4,fontsize=35,label=0.40,penwidth=14.99] 45 | 3 -- s0 [splines=none,colorscheme=paired10,color=1,minlen=4,fontsize=35,label=0.36,penwidth=13.93] 46 | dup0 -- s0 [splines=none,colorscheme=paired10,color=1,minlen=4,fontsize=35,label=0.51,penwidth=17.69] 47 | 4 -- dup0 [penwidth=5,style=dashed] 48 | } 49 | -------------------------------------------------------------------------------- /src/maxsolution.h: -------------------------------------------------------------------------------- 1 | /* 2 | * maxsolution.h 3 | * 4 | * Created on: 5-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef MAXSOLUTION_H 9 | #define MAXSOLUTION_H 10 | 11 | #include "utils.h" 12 | #include "realmatrix.h" 13 | #include "clonaltree.h" 14 | 15 | namespace vaff { 16 | 17 | class MaxSolution 18 | { 19 | public: 20 | struct Triple 21 | { 22 | RealMatrix _F; 23 | RealMatrix _U; 24 | ClonalTree _T; 25 | 26 | bool operator==(const Triple& other) const 27 | { 28 | return _U == other._U && _T == other._T && _F == other._F; 29 | } 30 | 31 | bool operator!=(const Triple& other) const 32 | { 33 | return !(operator==(other)); 34 | } 35 | 36 | friend std::ostream& operator<<(std::ostream& out, 37 | const Triple& triple); 38 | 39 | friend std::istream& operator>>(std::istream& in, 40 | Triple& triple); 41 | }; 42 | 43 | typedef std::vector TripleVector; 44 | typedef TripleVector::const_iterator TripleVectorIt; 45 | 46 | MaxSolution(const RealMatrix& F); 47 | 48 | MaxSolution(); 49 | 50 | void add(const Triple& triple) 51 | { 52 | _triples.push_back(triple); 53 | } 54 | 55 | const Triple& solution(int index) const 56 | { 57 | assert(0 <= index && index < _triples.size()); 58 | return _triples[index]; 59 | } 60 | 61 | int size() const 62 | { 63 | return _triples.size(); 64 | } 65 | 66 | void clear() 67 | { 68 | _triples.clear(); 69 | } 70 | 71 | bool present(const Triple& sol) const 72 | { 73 | for (TripleVectorIt it = _triples.begin(); it != _triples.end(); ++it) 74 | { 75 | if (*it == sol) 76 | { 77 | return true; 78 | } 79 | } 80 | 81 | return false; 82 | } 83 | 84 | const RealMatrix& getF() const 85 | { 86 | return _F; 87 | } 88 | 89 | void remapLabels(int max_cluster_size); 90 | 91 | double computeVafDelta(int sol_idx) const; 92 | 93 | void printVafDelta(int sol_idx, std::ostream& out) const; 94 | 95 | friend std::ostream& operator<<(std::ostream& out, 96 | const MaxSolution& solution); 97 | 98 | friend std::istream& operator>>(std::istream& in, 99 | MaxSolution& solution); 100 | 101 | private: 102 | RealMatrix _F; 103 | TripleVector _triples; 104 | 105 | typedef TripleVector::iterator TripleVectorNonConstIt; 106 | }; 107 | 108 | } // namespace vaff 109 | 110 | #endif // MAXSOLUTION_H -------------------------------------------------------------------------------- /src/baseancestrygraph.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * baseancestrygraph.cpp 3 | * 4 | * Created on: 10-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "baseancestrygraph.h" 9 | #include 10 | 11 | namespace vaff { 12 | 13 | BaseAncestryGraph::BaseAncestryGraph() 14 | : _G() 15 | , _columnToNode() 16 | , _nodeToColumn(_G) 17 | , _outDegree(_G) 18 | , _prob(_G) 19 | { 20 | } 21 | 22 | BaseAncestryGraph::BaseAncestryGraph(int n) 23 | : _G() 24 | , _columnToNode(n, lemon::INVALID) 25 | , _nodeToColumn(_G) 26 | , _outDegree(_G) 27 | , _prob(_G) 28 | { 29 | } 30 | 31 | void BaseAncestryGraph::writeDOT(std::ostream& out) const 32 | { 33 | out << "digraph G {" << std::endl; 34 | for (NodeIt v(_G); v != lemon::INVALID; ++v) 35 | { 36 | out << "\t" << _nodeToColumn[v] << std::endl; 37 | } 38 | 39 | for (ArcIt a(_G); a != lemon::INVALID; ++a) 40 | { 41 | Node s = _G.source(a); 42 | Node t = _G.target(a); 43 | 44 | out << "\t" << _nodeToColumn[s] << " -> " << _nodeToColumn[t] << std::endl; 45 | } 46 | out << "}" << std::endl; 47 | } 48 | 49 | void BaseAncestryGraph::contract(const StlIntMatrix& toOrginalColumns, 50 | BaseAncestryGraph& H) const 51 | { 52 | H._G.clear(); 53 | 54 | int n = toOrginalColumns.size(); 55 | H._G.reserveNode(n); 56 | H._columnToNode = NodeVector(n, lemon::INVALID); 57 | 58 | IntNodeMap toNewColumn(_G); 59 | for (int i = 0; i < n; ++i) 60 | { 61 | Node v_i = H._G.addNode(); 62 | H._nodeToColumn[v_i] = i; 63 | H._columnToNode[i] = v_i; 64 | 65 | const StlIntVector& S = toOrginalColumns[i]; 66 | for (StlIntVectorIt it = S.begin(); it != S.end(); ++it) 67 | { 68 | toNewColumn[_columnToNode[*it]] = i; 69 | } 70 | } 71 | 72 | StlBoolMatrix bitmap(n, StlBoolVector(n, false)); 73 | for (int i = 0; i < n; ++i) 74 | { 75 | bitmap[i][i] = true; 76 | } 77 | 78 | for (ArcIt a(_G); a != lemon::INVALID; ++a) 79 | { 80 | Node u = _G.source(a); 81 | Node v = _G.target(a); 82 | 83 | int index_uu = toNewColumn[u]; 84 | int index_vv = toNewColumn[v]; 85 | 86 | Node uu = H._columnToNode[index_uu]; 87 | Node vv = H._columnToNode[index_vv]; 88 | 89 | if (!bitmap[index_uu][index_vv]) 90 | { 91 | bitmap[index_uu][index_vv] = true; 92 | H._G.addArc(uu, vv); 93 | } 94 | } 95 | 96 | // for (ArcIt a(H._G); a != lemon::INVALID; ++a) 97 | // { 98 | // std::cout << H._nodeToColumn[H._G.source(a)] << " -> " << H._nodeToColumn[H._G.target(a)] << std::endl; 99 | // } 100 | } 101 | 102 | } // namespace vaff -------------------------------------------------------------------------------- /data/real/292_whole.txt: -------------------------------------------------------------------------------- 1 | gene_id 11 11 14 14 16 16 2 | HEATR7B2,5.0,41039005 117 28 100 35 186 39 3 | FAM21C,10.0,46281030 54 14 72 18 114 12 4 | NME7,1.0,169293537 103 27 92 46 221 57 5 | ABCF1,6.0,30550809 135 26 139 31 249 55 6 | AP4M1,7.0,99699527 66 23 119 31 141 48 7 | RAD54L2,3.0,51667926 55 23 73 34 142 34 8 | PTPN21,14.0,88951437 100 38 127 37 233 63 9 | COL19A1,6.0,70642708 33 6 48 14 82 18 10 | AB231703,11.0,64833998 66 9 74 11 115 20 11 | RAP1GAP,1.0,21939814 58 25 50 5 111 29 12 | PFAS,17.0,8160150 80 18 114 10 154 20 13 | CKM,19.0,45810232 85 10 112 0 153 14 14 | AIM1L,1.0,26665033 66 14 108 9 156 21 15 | SIGLEC10,19.0,51918061 140 55 171 67 252 89 16 | KPNA1,3.0,122182832 77 42 98 35 189 64 17 | DRP2,X,100507734 37 14 52 21 121 36 18 | TTN,2.0,179580421 326 70 421 47 635 105 19 | ASB15,7.0,123276954 56 22 69 14 129 41 20 | PLK5,19.0,1528142 85 31 138 28 191 41 21 | GNAO1,16.0,56279373 56 20 59 27 101 24 22 | FNDC1,6.0,159653591 261 17 23 | MMS22L,6.0,97715820 27 13 44 25 104 20 24 | GRXCR1(dist=555999),KCTD8(dist=587246),4.0,43588674 95 143 134 153 181 172 25 | SPEG,2.0,220343719 43 28 81 32 97 66 26 | CBS,21.0,44476094 97 88 138 99 248 166 27 | GRIN2A,16.0,10031924 264 62 244 35 432 76 28 | HTR7,10.0,92503477 148 8 173 3 248 6 29 | DPM3,1.0,155112801 163 23 205 32 324 54 30 | PSD2,5.0,139216391 190 14 218 5 31 | BEGAIN,14.0,101012852 168 36 180 45 305 67 32 | GGT6,17.0,4463016 45 10 70 15 91 14 33 | LMCD1,3.0,8590233 93 43 112 51 246 83 34 | CD40LG,X,135741382 402 59 509 40 678 81 35 | VPS13B,8.0,100514046 99 27 140 35 268 55 36 | OVGP1,1.0,111969772 89 26 110 24 168 32 37 | SSX5(dist=17843),SSX1(dist=40755),X,48074042 302 69 451 82 686 100 38 | EGFR,7.0,55259515 92 100 87 78 145 148 39 | C15orf52,15.0,40633086 130 29 126 39 192 56 40 | VPS4B,18.0,61078745 145 70 200 72 415 127 41 | PLEKHM1P,17.0,62830433 89 25 110 15 168 43 42 | HDGFL1,6.0,22570545 97 22 96 15 135 44 43 | SPATA5,4.0,124177208 168 50 215 53 381 104 44 | ZNF543,19.0,57840348 194 45 200 26 329 60 45 | PFAS,17.0,8160149 80 16 115 11 159 19 46 | CBFA2T3,16.0,88945810 145 8 47 | SLC35C2,20.0,44985235 47 14 87 17 118 31 48 | LOC146336,16.0,1116427 263 18 260 14 445 33 49 | SCN3B,11.0,123504698 45 14 52 19 127 36 50 | RSAD2,2.0,7027287 129 50 201 74 357 120 51 | LCT,2.0,136594241 149 28 162 21 291 54 52 | SPATA6,1.0,48790868 271 22 261 16 461 45 53 | COL6A6,3.0,130353496 47 17 70 16 121 42 54 | ATG9A,2.0,220089904 66 26 72 17 111 41 55 | SMURF1,7.0,98654967 128 34 171 49 311 42 56 | NM_001162367,7.0,150446794 301 35 387 33 635 40 57 | LOX;LOX,5.0,121405748 87 34 147 29 208 55 58 | CST11,20.0,23432530 91 53 133 58 216 81 59 | OR14A16,1.0,247978337 109 77 126 84 259 159 60 | PFAS,17.0,8167192 229 18 449 18 61 | KIAA1522,1.0,33233495 246 54 254 50 494 64 62 | CUTC,10.0,101499599 129 35 195 36 351 56 63 | -------------------------------------------------------------------------------- /data/real/292_deep.txt: -------------------------------------------------------------------------------- 1 | gene_id 11 11 14 14 16 16 2 | HEATR7B2,5.0,41039005 706 150 710 161 466 110 3 | FAM21C,10.0,46281030 395 98 431 66 237 41 4 | NME7,1.0,169293537 545 141 527 139 441 77 5 | ABCF1,6.0,30550809 738 225 799 157 783 170 6 | AP4M1,7.0,99699527 651 231 625 229 498 209 7 | RAD54L2,3.0,51667926 399 197 456 162 350 110 8 | PTPN21,14.0,88951437 754 204 801 169 767 155 9 | COL19A1,6.0,70642708 596 198 768 199 454 127 10 | AB231703,11.0,64833998 689 186 799 133 541 112 11 | RAP1GAP,1.0,21939814 370 110 347 113 254 63 12 | PFAS,17.0,8160150 691 127 901 60 622 78 13 | CKM,19.0,45810232 319 32 421 14 343 9 14 | AIM1L,1.0,26665033 501 81 648 73 410 47 15 | SIGLEC10,19.0,51918061 654 247 656 245 574 236 16 | KPNA1,3.0,122182832 484 204 547 188 342 110 17 | DRP2,X,100507734 664 166 570 133 415 79 18 | TTN,2.0,179580421 699 190 846 85 705 124 19 | ASB15,7.0,123276954 645 281 694 247 483 169 20 | PLK5,19.0,1528142 633 157 675 109 536 96 21 | GNAO1,16.0,56279373 678 276 664 279 542 189 22 | FNDC1,6.0,159653591 891 44 23 | MMS22L,6.0,97715820 492 190 623 155 426 93 24 | GRXCR1(dist=555999),KCTD8(dist=587246),4.0,43588674 443 516 430 543 480 449 25 | SPEG,2.0,220343719 275 114 292 145 201 81 26 | CBS,21.0,44476094 319 257 382 300 240 172 27 | GRIN2A,16.0,10031924 757 154 849 108 780 150 28 | HTR7,10.0,92503477 374 42 441 5 290 15 29 | DPM3,1.0,155112801 681 116 743 82 559 67 30 | PSD2,5.0,139216391 628 37 740 9 31 | BEGAIN,14.0,101012852 706 170 735 148 545 123 32 | GGT6,17.0,4463016 720 191 734 202 729 186 33 | LMCD1,3.0,8590233 668 259 682 261 596 271 34 | CD40LG,X,135741382 848 129 877 89 866 97 35 | VPS13B,8.0,100514046 690 248 701 184 515 160 36 | OVGP1,1.0,111969772 757 206 755 200 672 224 37 | SSX5(dist=17843),SSX1(dist=40755),X,48074042 758 187 822 127 634 93 38 | EGFR,7.0,55259515 307 380 345 392 274 244 39 | C15orf52,15.0,40633086 552 171 634 209 405 105 40 | VPS4B,18.0,61078745 681 272 692 220 580 155 41 | PLEKHM1P,17.0,62830433 758 208 735 219 610 161 42 | HDGFL1,6.0,22570545 710 228 814 144 728 220 43 | SPATA5,4.0,124177208 794 188 832 157 782 183 44 | ZNF543,19.0,57840348 326 97 417 68 277 50 45 | PFAS,17.0,8160149 695 124 900 59 629 79 46 | CBFA2T3,16.0,88945810 925 18 47 | SLC35C2,20.0,44985235 468 178 518 177 307 115 48 | LOC146336,16.0,1116427 872 62 885 50 869 55 49 | SCN3B,11.0,123504698 458 153 491 206 335 146 50 | RSAD2,2.0,7027287 478 199 658 225 413 130 51 | LCT,2.0,136594241 634 151 777 117 517 86 52 | SPATA6,1.0,48790868 890 46 899 68 863 76 53 | COL6A6,3.0,130353496 590 229 644 241 396 168 54 | ATG9A,2.0,220089904 436 175 474 223 352 116 55 | SMURF1,7.0,98654967 436 88 461 66 298 61 56 | NM_001162367,7.0,150446794 884 75 879 72 896 59 57 | LOX;LOX,5.0,121405748 751 184 780 184 570 127 58 | CST11,20.0,23432530 585 355 648 249 593 203 59 | OR14A16,1.0,247978337 469 405 460 415 465 358 60 | PFAS,17.0,8167192 865 86 797 25 61 | KIAA1522,1.0,33233495 821 122 817 113 703 83 62 | CUTC,10.0,101499599 708 166 774 106 572 97 63 | -------------------------------------------------------------------------------- /src/readcountmatrix.h: -------------------------------------------------------------------------------- 1 | /* 2 | * readcountmatrix.h 3 | * 4 | * Created on: 10-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef READCOUNTMATRIX_H 9 | #define READCOUNTMATRIX_H 10 | 11 | #include "matrix.h" 12 | #include "utils.h" 13 | #include "realintervalmatrix.h" 14 | 15 | namespace vaff { 16 | 17 | class ReadCountMatrix : public Matrix 18 | { 19 | public: 20 | ReadCountMatrix(); 21 | 22 | ReadCountMatrix(int m, int n); 23 | 24 | const StlIntMatrix& getC() const 25 | { 26 | // alternate 27 | return _C; 28 | } 29 | 30 | const StlIntMatrix& getD() const 31 | { 32 | // reference 33 | return _D; 34 | } 35 | 36 | int getAlt(int row, int col) const 37 | { 38 | assert(0 <= row && row < _m); 39 | assert(0 <= col && col < _n); 40 | 41 | return _C[row][col]; 42 | } 43 | 44 | int getRef(int row, int col) const 45 | { 46 | assert(0 <= row && row < _m); 47 | assert(0 <= col && col < _n); 48 | 49 | return _D[row][col]; 50 | } 51 | 52 | IntPair operator()(int row, int col) const 53 | { 54 | assert(0 <= row && row < _m); 55 | assert(0 <= col && col < _n); 56 | 57 | return std::make_pair(_C[row][col], _D[row][col]); 58 | } 59 | 60 | void set(int row, int col, int alt, int ref) 61 | { 62 | assert(0 <= row && row < _m); 63 | assert(0 <= col && col < _n); 64 | 65 | _C[row][col] = alt; 66 | _D[row][col] = ref; 67 | } 68 | 69 | double coverage() const 70 | { 71 | double res = 0; 72 | for (int i = 0; i < _m; ++i) 73 | { 74 | for (int j = 0; j < _n; ++j) 75 | { 76 | res += _C[i][j] + _D[i][j]; 77 | } 78 | } 79 | return res / (_m * _n); 80 | } 81 | 82 | void remapLabels(const StlIntMatrix& toOrgCols, 83 | const ReadCountMatrix& orgR, 84 | int max_cluster_size = 10); 85 | 86 | void computeConfidenceIntervals(RealIntervalMatrix& CI, double gamma) const; 87 | 88 | void computePointEstimates(RealMatrix& F) const; 89 | 90 | ReadCountMatrix collapse(StlIntMatrix& toOrgColumns) const; 91 | 92 | bool operator==(const ReadCountMatrix& other) const 93 | { 94 | return _m == other._m && _n == other._n && _C == other._C && _D == other._D; 95 | } 96 | 97 | bool operator!=(const ReadCountMatrix& other) const 98 | { 99 | return !this->operator==(other); 100 | } 101 | 102 | friend std::ostream& operator<<(std::ostream& out, 103 | const ReadCountMatrix& matrix); 104 | 105 | friend std::istream& operator>>(std::istream& in, 106 | ReadCountMatrix& matrix); 107 | 108 | protected: 109 | StlIntMatrix _C; 110 | StlIntMatrix _D; 111 | }; 112 | 113 | } // namespace vaff 114 | 115 | #endif // READCOUNTMATRIX_H 116 | -------------------------------------------------------------------------------- /src/ppmatrix.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * ppmatrix.cpp 3 | * 4 | * Created on: 22-dec-2014 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "ppmatrix.h" 9 | #include 10 | 11 | namespace vaff { 12 | 13 | PpMatrix::PpMatrix() 14 | : Matrix() 15 | , _C() 16 | , _prob() 17 | { 18 | } 19 | 20 | PpMatrix::PpMatrix(int m, int n) 21 | : Matrix(m, n) 22 | , _C(m, StlBoolVector(n, false)) 23 | , _prob(m, 1) 24 | { 25 | } 26 | 27 | bool PpMatrix::isConflictFree() const 28 | { 29 | for (int col1 = 0; col1 < _n; ++col1) 30 | { 31 | for (int col2 = col1 + 1; col2 < _n; ++col2) 32 | { 33 | if (hasConflict(col1, col2)) 34 | { 35 | return false; 36 | } 37 | } 38 | } 39 | 40 | return true; 41 | } 42 | 43 | bool PpMatrix::hasConflict(int col1, int col2) const 44 | { 45 | assert(0 <= col1 && col1 < _n); 46 | assert(0 <= col2 && col2 < _n); 47 | bool one_one = false, one_zero = false, zero_one = false; 48 | 49 | for (int i = 0; i < _m; ++i) 50 | { 51 | one_one |= _C[i][col1] && _C[i][col2]; 52 | one_zero |= _C[i][col1] && !_C[i][col2]; 53 | zero_one |= !_C[i][col1] && _C[i][col2]; 54 | } 55 | 56 | return one_one && one_zero && zero_one; 57 | } 58 | 59 | bool PpMatrix::isContained(int col1, int col2) const 60 | { 61 | assert(0 <= col1 && col1 < _n); 62 | assert(0 <= col2 && col2 < _n); 63 | 64 | for (int i = 0; i < _m; ++i) 65 | { 66 | if (_C[i][col1] && !_C[i][col2]) 67 | return false; 68 | } 69 | 70 | return true; 71 | } 72 | 73 | bool PpMatrix::isDisjoint(int col1, int col2) const 74 | { 75 | assert(0 <= col1 && col1 < _n); 76 | assert(0 <= col2 && col2 < _n); 77 | 78 | for (int i = 0; i < _m; ++i) 79 | { 80 | if (_C[i][col1] && _C[i][col2]) 81 | return false; 82 | } 83 | 84 | return true; 85 | } 86 | 87 | std::ostream& operator<<(std::ostream& out, 88 | const PpMatrix& matrix) 89 | { 90 | out << matrix._C; 91 | out << std::endl; 92 | 93 | for (int j = 0; j < matrix._m; ++j) 94 | { 95 | out << matrix._prob[j] << " "; 96 | } 97 | out << std::endl; 98 | 99 | return out; 100 | } 101 | 102 | std::istream& operator>>(std::istream& in, 103 | PpMatrix& matrix) 104 | { 105 | in >> matrix._C; 106 | 107 | matrix._m = matrix._C.size(); 108 | matrix._n = matrix._C.empty() ? 0 : matrix._C.front().size(); 109 | matrix._rowLabel.resize(matrix._m); 110 | matrix._colLabel.resize(matrix._n); 111 | 112 | matrix._prob = StlDoubleVector(matrix._m, 1); 113 | 114 | std::string line; 115 | vaff::getline(in, line); 116 | vaff::getline(in, line); 117 | std::stringstream ss(line); 118 | for (int j = 0; j < matrix._m; ++j) 119 | { 120 | ss >> matrix._prob[j]; 121 | } 122 | 123 | return in; 124 | } 125 | 126 | } // namespace vaff 127 | -------------------------------------------------------------------------------- /src/realintervalmatrix.h: -------------------------------------------------------------------------------- 1 | /* 2 | * realintervalmatrix.h 3 | * 4 | * Created on: 7-jan-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef REALINTERVALMATRIX_H 9 | #define REALINTERVALMATRIX_H 10 | 11 | #include "matrix.h" 12 | #include "utils.h" 13 | #include "realmatrix.h" 14 | 15 | namespace vaff { 16 | 17 | class RealIntervalMatrix : public Matrix 18 | { 19 | public: 20 | RealIntervalMatrix(); 21 | 22 | RealIntervalMatrix(int m, int n); 23 | 24 | const StlRealIntervalMatrix& getMatrix() const 25 | { 26 | return _C; 27 | } 28 | 29 | const RealInterval& operator()(int row, int col) const 30 | { 31 | assert(0 <= row && row < _m); 32 | assert(0 <= col && col < _n); 33 | 34 | return _C[row][col]; 35 | } 36 | 37 | void set(int row, int col, RealInterval interval) 38 | { 39 | assert(0 <= row && row < _m); 40 | assert(0 <= col && col < _n); 41 | 42 | _C[row][col] = interval; 43 | } 44 | 45 | bool operator==(const RealIntervalMatrix& other) const 46 | { 47 | return _m == other._m && _n == other._n && _C == other._C; 48 | } 49 | 50 | bool operator!=(const RealIntervalMatrix& other) const 51 | { 52 | return !this->operator==(other); 53 | } 54 | 55 | double meanIntervalLength(bool excludeTight) const 56 | { 57 | double mean = 0; 58 | int count = 0; 59 | 60 | for (int i = 0; i < _m; ++i) 61 | { 62 | for (int j = 0; j < _n; ++j) 63 | { 64 | if (!excludeTight || _C[i][j].first != _C[i][j].second) 65 | { 66 | mean += _C[i][j].second - _C[i][j].first; 67 | ++count; 68 | } 69 | } 70 | } 71 | 72 | return mean / count; 73 | } 74 | 75 | int tightAndZeroIntervalCount() const 76 | { 77 | int count = 0; 78 | for (int i = 0; i < _m; ++i) 79 | { 80 | for (int j = 0; j < _n; ++j) 81 | { 82 | if (_C[i][j].first == 0 && _C[i][j].second == 0) 83 | { 84 | ++count; 85 | } 86 | } 87 | } 88 | return count; 89 | } 90 | 91 | int tightIntervalCount() const 92 | { 93 | int count = 0; 94 | for (int i = 0; i < _m; ++i) 95 | { 96 | for (int j = 0; j < _n; ++j) 97 | { 98 | if (_C[i][j].first == _C[i][j].second) 99 | { 100 | ++count; 101 | } 102 | } 103 | } 104 | return count; 105 | } 106 | 107 | void obtainPointEstimates(RealMatrix& F) const; 108 | 109 | friend std::ostream& operator<<(std::ostream& out, 110 | const RealIntervalMatrix& matrix); 111 | 112 | friend std::istream& operator>>(std::istream& in, 113 | RealIntervalMatrix& matrix); 114 | 115 | protected: 116 | StlRealIntervalMatrix _C; 117 | }; 118 | 119 | } 120 | 121 | #endif // REALINTERVALMATRIX_H -------------------------------------------------------------------------------- /data/real/RMH002.txt: -------------------------------------------------------------------------------- 1 | gene_id R1 R1 R2 R2 R6 R6 R3 R3 R7 R7 2 | CYR61,chr1:86047115 1740 458 1334 53 582 98 1271 435 712 132 3 | CENPF,chr1:214816224 4420 944 2953 112 1329 97 3620 0 1724 247 4 | MARCO,chr2:119751996 5479 1163 3775 144 1610 174 3522 1005 2253 342 5 | WDR33,chr2:128466334 5254 915 3409 130 1705 135 3399 772 1546 703 6 | ZDHHC3,chr3:45000715 4284 1210 3419 114 1712 418 2484 946 1075 1024 7 | GNPDA2,chr4:44709934 4306 919 2407 95 885 103 3022 811 1136 407 8 | DCBLD1,chr6:117841041 4842 982 2886 101 1489 170 3028 933 1089 397 9 | KCNB2,chr8:73849748 4002 807 2203 80 1069 195 2624 745 1108 508 10 | LDB3,chr10:88451726 4702 955 3474 105 1224 99 3261 974 1032 1084 11 | GAS6,chr13:114566625 2403 635 1770 62 639 89 2088 651 1029 352 12 | NPEPPS,chr17:45696476 4574 1028 2728 92 1009 106 2911 793 1339 370 13 | C17orf90,chr17:79632553 5026 1135 3481 137 1645 134 4864 886 2027 518 14 | CSMD3,chr8:113349840 5701 0 2554 81 1139 238 3067 876 931 416 15 | SHANK1,chr19:51219681 5661 0 3396 123 1248 157 2705 731 1394 421 16 | GLB1,chr3:33099620 540 0 302 0 146 33 260 112 85 55 17 | DPP6,chr7:154561175 7186 0 3999 0 1472 217 3339 1029 2452 938 18 | ASAP1,chr8:131140197 6101 0 3172 0 1507 283 3535 947 1996 734 19 | CYP17A1,chr10:104590461 4683 0 2447 0 1153 130 2268 643 587 556 20 | FBN2,chr5:127728882 2651 0 1056 0 582 42 1730 0 399 107 21 | RIMS2,chr8:105263327 5705 0 2815 0 1333 96 2862 760 1307 0 22 | CTNNA2,chr2:80136761 2018 0 1070 0 604 0 1049 271 308 157 23 | UROC1,chr3:126226811 6874 0 4055 0 1888 0 3545 498 1484 173 24 | DOT1L,chr19:2226271 5248 0 3381 0 1118 0 3076 841 1558 780 25 | PTPRT,chr20:41419958 7274 0 3998 0 2277 0 6482 130 2944 591 26 | HIVEP3,chr1:42048662 4885 1190 3420 0 1447 0 4049 0 2179 0 27 | MTMR11,chr1:149903893 6384 1315 4468 0 2042 0 5177 0 2413 0 28 | ATL2,chr2:38525435 5272 406 2786 0 1544 0 4059 0 1713 0 29 | TAAR1,chr6:132966457 4798 950 2668 0 1262 0 4370 0 1798 0 30 | CDH23,chr10:73464783 2913 185 1812 0 767 0 1897 0 793 0 31 | GRID1,chr10:87407144 5334 1134 3764 0 1715 0 4898 0 2470 0 32 | CILP,chr15:65489101 5567 1155 3940 0 2194 0 5041 0 2252 0 33 | FAM129C,chr19:17652964 3963 832 2706 0 1221 0 3017 0 1690 0 34 | ITPR1,chr3:4878510 5972 0 3657 0 1268 260 4055 0 2383 0 35 | ZNF518B,chr4:10445618 5918 0 3032 0 1656 150 4282 0 1647 0 36 | KIAA1217,chr10:24820837 6392 0 3285 0 1368 139 4379 0 2127 0 37 | TTLL9,chr20:30497690 2415 0 1540 0 712 85 1705 0 1152 0 38 | CCKBR,chr11:6292024 3953 0 1980 0 969 0 2190 602 979 0 39 | GOLGA3,chr12:133358952 6727 0 4173 0 1896 0 4241 952 1855 0 40 | AIFM3,chr22:21328822 4709 0 2680 0 942 0 2619 736 1569 0 41 | ROCK1,chr18:18608851 7325 0 3531 0 1582 0 3905 1076 2508 0 42 | BSN,chr3:49688508 5274 0 3858 0 1493 0 3450 0 1299 1119 43 | HTT,chr4:3189513 5247 0 2737 0 1068 0 3548 0 1134 115 44 | PCM1,chr8:17827164 6298 0 2913 0 1335 0 3588 0 1203 279 45 | SYBU,chr8:110588046 6421 0 3264 0 1732 0 4309 0 1563 339 46 | OR51V1,chr11:5221789 5728 0 2775 0 1412 0 4093 0 923 377 47 | C12orf40,chr12:40114846 6591 0 2951 0 1421 0 5261 0 1073 248 48 | TP53,chr17:7577018 6806 0 3776 0 1609 0 4937 0 1443 698 49 | ELAC1,chr18:48513396 6977 0 3756 0 1771 0 4796 0 1490 580 50 | -------------------------------------------------------------------------------- /src/ppmatrix.h: -------------------------------------------------------------------------------- 1 | /* 2 | * ppmatrix.h 3 | * 4 | * Created on: 22-dec-2014 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #ifndef PPMATRIX_H 9 | #define PPMATRIX_H 10 | 11 | #include "matrix.h" 12 | #include "utils.h" 13 | 14 | namespace vaff { 15 | 16 | class PpMatrix : public Matrix 17 | { 18 | public: 19 | PpMatrix(); 20 | 21 | PpMatrix(int m, int n); 22 | 23 | const StlBoolMatrix& getMatrix() const 24 | { 25 | return _C; 26 | } 27 | 28 | bool operator()(int row, int col) const 29 | { 30 | assert(0 <= row && row < _m); 31 | assert(0 <= col && col < _n); 32 | 33 | return _C[row][col]; 34 | } 35 | 36 | void set(int row, int col, bool val) 37 | { 38 | assert(0 <= row && row < _m); 39 | assert(0 <= col && col < _n); 40 | 41 | _C[row][col] = val; 42 | } 43 | 44 | int rowSum(int row) const 45 | { 46 | assert(0 <= row && row < _m); 47 | 48 | int res = 0; 49 | for (int j = 0; j < _n; ++j) 50 | { 51 | if (_C[row][j]) 52 | { 53 | ++res; 54 | } 55 | } 56 | 57 | return res; 58 | } 59 | 60 | int isRowContained(int row1, int row2) const 61 | { 62 | assert(0 <= row1 && row1 < _m); 63 | assert(0 <= row2 && row2 < _m); 64 | 65 | int diff = 0; 66 | for (int j = 0; j < _n; ++j) 67 | { 68 | int val1 = _C[row1][j] ? 1 : 0; 69 | int val2 = _C[row2][j] ? 1 : 0; 70 | 71 | if (val1 == 1 && val2 == 0) 72 | { 73 | return -1; 74 | } 75 | else if (val1 == 0 && val2 == 1) 76 | { 77 | ++diff; 78 | } 79 | } 80 | 81 | return diff; 82 | } 83 | 84 | bool isConflictFree() const; 85 | 86 | bool hasConflict(int col1, int col2) const; 87 | 88 | bool isContained(int col1, int col2) const; 89 | 90 | bool isDisjoint(int col1, int col2) const; 91 | 92 | bool operator==(const PpMatrix& other) const 93 | { 94 | return _m == other._m && _n == other._n && _C == other._C; 95 | } 96 | 97 | bool operator!=(const PpMatrix& other) const 98 | { 99 | return !this->operator==(other); 100 | } 101 | 102 | unsigned long twoPowerColSum(int col) const 103 | { 104 | assert(0 <= col && col < _n); 105 | 106 | unsigned long res = 0; 107 | for (int i = 0; i < _m; ++i) 108 | { 109 | if (_C[i][col]) 110 | { 111 | res |= (1 << i); 112 | } 113 | } 114 | 115 | return res; 116 | } 117 | 118 | double prob(int j) const 119 | { 120 | assert(0 <= j && j < _m); 121 | return _prob[j]; 122 | } 123 | 124 | void setProb(int j, double p) 125 | { 126 | assert(0 <= j && j < _m); 127 | _prob[j] = p; 128 | } 129 | 130 | friend std::ostream& operator<<(std::ostream& out, 131 | const PpMatrix& matrix); 132 | 133 | friend std::istream& operator>>(std::istream& in, 134 | PpMatrix& matrix); 135 | 136 | protected: 137 | StlBoolMatrix _C; 138 | StlDoubleVector _prob; 139 | }; 140 | 141 | } // namespace vaff 142 | 143 | #endif // PPMATRIX_H -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_8.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 34 3 51 0 46 0 37 0 3 | Mut_1 52 3 50 0 54 0 35 0 4 | Mut_2 34 4 56 0 66 0 47 0 5 | Mut_3 53 6 46 0 39 0 44 0 6 | Mut_4 39 2 53 0 60 0 53 0 7 | Mut_5 45 10 51 0 41 0 48 0 8 | Mut_6 46 6 54 0 58 0 50 0 9 | Mut_7 45 6 51 0 49 0 48 0 10 | Mut_8 42 6 44 0 59 0 53 0 11 | Mut_9 41 7 51 0 56 0 53 0 12 | Mut_10 48 2 42 0 46 0 56 0 13 | Mut_11 51 8 56 0 47 0 46 0 14 | Mut_12 50 4 40 0 39 0 54 0 15 | Mut_13 55 7 44 0 51 0 53 0 16 | Mut_14 42 6 48 0 60 0 51 0 17 | Mut_15 41 7 56 0 44 7 37 0 18 | Mut_16 46 3 47 0 34 10 46 0 19 | Mut_17 44 9 59 0 41 2 53 0 20 | Mut_18 48 0 41 0 42 3 51 11 21 | Mut_19 47 0 44 0 46 0 46 9 22 | Mut_20 47 0 37 0 52 0 46 4 23 | Mut_21 45 0 51 0 45 0 53 6 24 | Mut_22 68 0 47 0 49 0 49 5 25 | Mut_23 46 0 47 0 43 3 37 5 26 | Mut_24 55 0 52 0 42 1 45 6 27 | Mut_25 52 0 57 0 53 3 45 10 28 | Mut_26 34 0 49 0 49 2 47 2 29 | Mut_27 50 0 60 0 49 1 45 4 30 | Mut_28 50 0 53 0 54 3 43 8 31 | Mut_29 46 0 57 0 39 0 38 3 32 | Mut_30 51 0 44 0 54 1 31 9 33 | Mut_31 21 20 25 20 27 18 34 15 34 | Mut_32 33 16 44 16 24 21 27 15 35 | Mut_33 35 16 26 16 27 23 31 23 36 | Mut_34 27 14 37 16 23 14 35 23 37 | Mut_35 29 23 34 20 27 20 35 14 38 | Mut_36 37 19 29 17 31 27 33 20 39 | Mut_37 31 15 32 20 31 17 25 24 40 | Mut_38 32 21 32 10 28 14 34 17 41 | Mut_39 28 19 34 20 24 24 32 20 42 | Mut_40 35 15 18 19 25 25 33 22 43 | Mut_41 23 19 41 11 29 24 32 32 44 | Mut_42 49 4 53 0 45 0 48 0 45 | Mut_43 50 2 62 0 65 0 39 0 46 | Mut_44 38 5 43 0 56 0 44 0 47 | Mut_45 42 5 54 1 40 0 58 0 48 | Mut_46 48 4 52 0 67 0 52 0 49 | Mut_47 41 2 41 1 63 0 51 0 50 | Mut_48 57 0 44 11 45 0 25 16 51 | Mut_49 51 0 40 10 53 0 45 11 52 | Mut_50 62 0 33 9 51 0 37 18 53 | Mut_51 44 0 43 9 53 0 40 4 54 | Mut_52 50 0 39 9 55 0 23 16 55 | Mut_53 62 0 43 7 60 0 34 13 56 | Mut_54 42 0 32 5 43 0 33 10 57 | Mut_55 50 0 53 7 45 0 37 16 58 | Mut_56 32 0 40 14 41 0 43 10 59 | Mut_57 44 6 43 9 38 0 59 0 60 | Mut_58 49 2 49 8 55 0 50 1 61 | Mut_59 41 3 42 9 40 0 58 0 62 | Mut_60 53 2 34 7 47 0 46 1 63 | Mut_61 46 2 47 6 45 0 51 0 64 | Mut_62 36 3 36 4 54 0 50 0 65 | Mut_63 44 3 44 15 62 0 52 1 66 | Mut_64 56 3 42 2 60 0 46 0 67 | Mut_65 49 2 47 11 45 0 57 0 68 | Mut_66 43 4 33 9 61 2 45 5 69 | Mut_67 31 8 38 10 48 1 53 6 70 | Mut_68 50 6 50 3 52 1 47 12 71 | Mut_69 35 5 42 5 35 0 52 8 72 | Mut_70 51 11 33 4 56 0 46 3 73 | Mut_71 39 12 42 3 53 1 53 6 74 | Mut_72 48 8 31 13 49 1 45 14 75 | Mut_73 28 5 46 4 49 0 48 12 76 | Mut_74 51 9 47 7 53 1 40 3 77 | Mut_75 37 6 46 6 59 1 46 6 78 | Mut_76 38 8 38 4 42 1 45 7 79 | Mut_77 42 9 44 12 52 0 40 5 80 | Mut_78 39 11 51 5 53 2 42 2 81 | Mut_79 41 11 57 5 61 0 38 9 82 | Mut_80 33 8 39 7 60 1 42 7 83 | Mut_81 43 7 42 7 54 2 43 8 84 | Mut_82 39 6 44 7 47 2 55 5 85 | Mut_83 39 10 37 10 41 1 44 6 86 | Mut_84 57 8 41 4 42 1 46 7 87 | Mut_85 39 10 38 13 49 1 52 10 88 | Mut_86 42 12 45 7 51 0 43 8 89 | Mut_87 51 11 49 12 53 0 33 11 90 | Mut_88 31 11 42 12 42 0 47 9 91 | Mut_89 40 8 35 12 35 1 38 3 92 | Mut_90 29 6 42 6 49 1 41 4 93 | Mut_91 45 3 43 9 43 0 37 0 94 | Mut_92 58 4 39 9 54 0 64 0 95 | Mut_93 46 4 32 10 51 0 52 0 96 | Mut_94 45 2 44 11 59 0 68 0 97 | Mut_95 54 2 36 9 40 0 40 0 98 | Mut_96 41 3 40 6 51 0 42 0 99 | Mut_97 50 1 39 7 56 0 47 0 100 | Mut_98 46 3 43 6 34 0 55 0 101 | Mut_99 44 3 42 7 56 0 40 0 102 | -------------------------------------------------------------------------------- /src/analysesolution.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * analysesolution.cpp 3 | * 4 | * Created on: 11-mar-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "utils.h" 9 | #include "maxsolution.h" 10 | #include "solutiongraph.h" 11 | #include "ancestrymatrix.h" 12 | #include "probancestrygraph.h" 13 | #include "comparison.h" 14 | #include 15 | #include 16 | #include 17 | 18 | using namespace vaff; 19 | 20 | void printUsage(const char* argv0, std::ostream& out) 21 | { 22 | out << "Usage: " << argv0 << " where" << std::endl 23 | << " is the solution file (use '-' for stdin)" << std::endl 24 | << " is the reference solution" << std::endl 25 | << " is the solution to be used as a whitelist" << std::endl; 26 | out << "Output:\n" 27 | " coverage\n" 28 | " delta F\n" 29 | " delta U\n" 30 | " recall clustered\n" 31 | " recall ancestral\n" 32 | " recall incomparable\n" 33 | " accuracy clustered\n" 34 | " accuracy ancestral\n" 35 | " accuracy incomparable" << std::endl; 36 | } 37 | 38 | int main(int argc, char** argv) 39 | { 40 | if (argc != 4) 41 | { 42 | printUsage(argv[0], std::cerr); 43 | return 1; 44 | } 45 | 46 | MaxSolution solution; 47 | { 48 | if (strcmp(argv[1], "-")) 49 | { 50 | std::ifstream in(argv[1]); 51 | if (!in.good()) 52 | { 53 | std::cerr << "Error: failed to open '" << argv[1] << "' for reading" << std::endl; 54 | return 1; 55 | } 56 | in >> solution; 57 | in.close(); 58 | } 59 | else 60 | { 61 | std::cin >> solution; 62 | } 63 | } 64 | 65 | MaxSolution refSolution; 66 | { 67 | std::ifstream in(argv[2]); 68 | if (!in.good()) 69 | { 70 | std::cerr << "Error: failed to open '" << argv[2] << "' for reading" << std::endl; 71 | return 1; 72 | } 73 | in >> refSolution; 74 | in.close(); 75 | } 76 | 77 | MaxSolution whitelistSolution; 78 | { 79 | std::ifstream in(argv[3]); 80 | if (!in.good()) 81 | { 82 | std::cerr << "Error: failed to open '" << argv[3] << "' for reading" << std::endl; 83 | return 1; 84 | } 85 | in >> whitelistSolution; 86 | in.close(); 87 | } 88 | 89 | Comparison comparison(refSolution, solution.solution(0), whitelistSolution.solution(0)); 90 | 91 | double coverage = comparison.coverage(); 92 | 93 | double deltaF = comparison.deltaF(); 94 | double deltaU = comparison.deltaU(); 95 | 96 | double clustered, ancestral, incomparable; 97 | comparison.recallB(clustered, ancestral, incomparable); 98 | 99 | double clustered_a, ancestral_a, incomparable_a; 100 | comparison.accuracyB(clustered_a, ancestral_a, incomparable_a); 101 | 102 | std::cout << coverage << "\t" 103 | << deltaF << "\t" 104 | << deltaU << "\t" 105 | << clustered << "\t" 106 | << ancestral << "\t" 107 | << incomparable << "\t" 108 | << clustered_a << "\t" 109 | << ancestral_a << "\t" 110 | << incomparable_a << std::endl; 111 | 112 | return 0; 113 | } -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_6.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 65 0 38 3 44 1 28 14 3 | Mut_1 54 0 52 3 50 3 37 20 4 | Mut_2 46 2 61 0 52 0 45 1 5 | Mut_3 44 2 45 0 49 0 52 1 6 | Mut_4 54 0 50 0 47 0 50 0 7 | Mut_5 47 1 37 0 53 0 56 1 8 | Mut_6 44 3 55 0 47 0 38 1 9 | Mut_7 46 3 52 0 59 0 40 1 10 | Mut_8 46 2 55 0 49 0 48 1 11 | Mut_9 45 3 48 0 44 0 47 0 12 | Mut_10 49 2 55 0 41 0 33 2 13 | Mut_11 58 1 50 0 48 0 47 0 14 | Mut_12 47 1 42 0 48 0 49 0 15 | Mut_13 48 0 61 0 54 0 49 1 16 | Mut_14 53 2 47 0 42 0 48 0 17 | Mut_15 51 3 64 0 51 0 48 3 18 | Mut_16 50 1 43 0 49 0 46 3 19 | Mut_17 39 2 49 0 41 0 55 1 20 | Mut_18 43 0 43 0 57 0 47 2 21 | Mut_19 51 0 42 0 47 0 47 1 22 | Mut_20 45 2 54 0 52 0 58 1 23 | Mut_21 48 0 50 0 48 0 50 0 24 | Mut_22 46 1 47 0 46 0 48 2 25 | Mut_23 42 0 45 0 58 0 50 1 26 | Mut_24 47 1 46 0 43 0 51 1 27 | Mut_25 48 3 29 0 40 0 53 1 28 | Mut_26 38 2 44 0 45 0 47 2 29 | Mut_27 51 4 58 0 54 0 42 1 30 | Mut_28 48 0 48 0 48 0 43 0 31 | Mut_29 38 3 56 0 40 0 60 2 32 | Mut_30 46 3 41 0 38 0 39 3 33 | Mut_31 56 1 43 0 51 0 51 1 34 | Mut_32 45 2 48 0 50 0 51 1 35 | Mut_33 41 3 47 0 52 0 46 2 36 | Mut_34 68 2 45 0 41 0 43 1 37 | Mut_35 51 3 48 0 54 0 52 1 38 | Mut_36 46 2 62 0 53 0 56 0 39 | Mut_37 45 2 40 0 45 0 41 2 40 | Mut_38 48 1 55 0 69 0 50 0 41 | Mut_39 41 3 48 0 52 0 56 2 42 | Mut_40 45 0 51 0 45 0 45 1 43 | Mut_41 54 2 47 0 44 0 55 1 44 | Mut_42 42 1 45 0 60 0 57 2 45 | Mut_43 46 3 48 0 41 0 43 0 46 | Mut_44 39 0 56 0 47 0 48 2 47 | Mut_45 52 3 54 0 46 0 57 2 48 | Mut_46 52 2 32 21 40 3 22 23 49 | Mut_47 43 2 34 14 45 1 24 29 50 | Mut_48 47 2 34 20 31 5 22 19 51 | Mut_49 46 1 26 16 49 1 39 17 52 | Mut_50 57 2 27 21 41 1 24 18 53 | Mut_51 40 2 33 9 40 2 24 16 54 | Mut_52 48 1 44 15 37 0 38 15 55 | Mut_53 47 4 39 15 59 0 36 17 56 | Mut_54 57 2 35 20 62 1 31 26 57 | Mut_55 58 1 27 21 42 1 24 14 58 | Mut_56 57 3 38 18 39 2 24 20 59 | Mut_57 51 3 22 17 57 3 26 20 60 | Mut_58 43 1 28 23 63 3 40 18 61 | Mut_59 58 3 29 22 43 2 19 18 62 | Mut_60 40 1 38 13 41 2 35 23 63 | Mut_61 50 4 29 7 54 0 48 0 64 | Mut_62 36 2 45 9 61 0 42 0 65 | Mut_63 27 29 38 26 36 13 29 20 66 | Mut_64 36 23 27 19 46 14 28 24 67 | Mut_65 33 21 32 19 41 13 30 18 68 | Mut_66 30 13 29 21 41 18 27 30 69 | Mut_67 36 18 35 22 27 9 25 21 70 | Mut_68 27 29 40 21 39 19 29 23 71 | Mut_69 20 19 30 18 45 13 26 23 72 | Mut_70 28 19 30 16 38 6 37 25 73 | Mut_71 26 25 23 29 27 16 24 20 74 | Mut_72 25 30 28 15 31 10 34 21 75 | Mut_73 24 22 24 27 40 13 31 12 76 | Mut_74 27 16 30 20 41 10 22 23 77 | Mut_75 22 28 32 18 39 15 30 19 78 | Mut_76 35 24 30 17 40 16 18 16 79 | Mut_77 26 22 26 20 30 11 29 19 80 | Mut_78 62 0 46 5 35 9 44 0 81 | Mut_79 49 0 51 5 44 9 44 0 82 | Mut_80 43 0 42 5 44 6 55 0 83 | Mut_81 55 0 40 8 36 16 55 0 84 | Mut_82 58 0 41 3 32 10 50 0 85 | Mut_83 46 0 47 3 53 10 55 0 86 | Mut_84 47 0 43 0 46 0 49 5 87 | Mut_85 34 0 32 1 36 0 37 3 88 | Mut_86 53 0 46 2 53 0 50 5 89 | Mut_87 47 0 32 1 39 0 48 3 90 | Mut_88 33 0 50 3 52 0 45 3 91 | Mut_89 51 0 39 1 50 0 49 8 92 | Mut_90 52 0 43 1 61 0 51 4 93 | Mut_91 41 0 36 5 46 0 65 5 94 | Mut_92 49 0 51 7 42 0 39 7 95 | Mut_93 50 0 57 0 53 0 36 6 96 | Mut_94 48 0 50 0 45 1 41 14 97 | Mut_95 54 0 62 0 50 1 41 14 98 | Mut_96 54 0 49 0 25 1 41 14 99 | Mut_97 50 0 46 0 45 3 49 17 100 | Mut_98 52 0 53 0 50 2 39 14 101 | Mut_99 39 0 37 3 33 12 54 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_5.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 59 0 51 0 31 4 45 0 3 | Mut_1 49 1 52 0 28 14 47 0 4 | Mut_2 49 0 49 0 50 8 58 0 5 | Mut_3 41 14 55 1 44 0 45 0 6 | Mut_4 35 17 51 2 46 0 35 0 7 | Mut_5 43 16 52 0 46 0 47 0 8 | Mut_6 30 14 43 2 35 0 46 0 9 | Mut_7 28 15 54 1 52 0 56 0 10 | Mut_8 30 15 39 0 45 0 56 0 11 | Mut_9 39 10 46 5 43 0 41 0 12 | Mut_10 35 13 60 3 33 0 53 0 13 | Mut_11 43 17 41 1 52 0 48 0 14 | Mut_12 35 19 37 2 60 0 47 0 15 | Mut_13 34 17 45 1 42 0 58 0 16 | Mut_14 41 16 49 1 57 0 43 0 17 | Mut_15 34 11 46 1 44 0 60 0 18 | Mut_16 17 30 42 8 30 24 42 16 19 | Mut_17 19 25 55 7 34 25 39 12 20 | Mut_18 30 22 44 15 29 21 25 11 21 | Mut_19 26 20 45 9 27 20 36 17 22 | Mut_20 52 0 51 0 45 6 41 0 23 | Mut_21 47 0 39 0 44 11 51 0 24 | Mut_22 58 0 64 0 37 13 57 0 25 | Mut_23 47 0 40 0 40 8 49 0 26 | Mut_24 62 0 49 0 44 8 42 0 27 | Mut_25 68 0 45 0 42 9 46 0 28 | Mut_26 46 0 53 0 37 13 50 0 29 | Mut_27 42 0 46 0 37 12 49 0 30 | Mut_28 48 1 63 0 38 9 44 0 31 | Mut_29 52 0 52 0 44 11 48 0 32 | Mut_30 52 0 42 0 37 11 51 0 33 | Mut_31 40 0 47 0 31 8 37 0 34 | Mut_32 37 0 54 0 33 6 56 0 35 | Mut_33 50 1 53 0 36 12 58 0 36 | Mut_34 48 0 48 0 41 9 49 0 37 | Mut_35 47 0 50 0 34 6 41 0 38 | Mut_36 54 0 46 0 33 7 52 0 39 | Mut_37 54 0 56 0 40 9 56 0 40 | Mut_38 31 0 45 0 40 7 57 0 41 | Mut_39 49 1 42 0 41 14 53 0 42 | Mut_40 51 0 41 0 37 10 53 0 43 | Mut_41 47 0 38 0 38 12 52 0 44 | Mut_42 45 0 57 0 42 8 61 0 45 | Mut_43 31 9 50 0 57 0 47 0 46 | Mut_44 53 9 53 0 54 0 47 0 47 | Mut_45 40 6 45 0 60 0 47 0 48 | Mut_46 42 8 57 0 53 0 45 0 49 | Mut_47 35 9 58 0 41 0 59 0 50 | Mut_48 34 12 52 0 47 0 45 0 51 | Mut_49 35 6 44 0 46 0 40 0 52 | Mut_50 34 9 49 0 56 0 39 0 53 | Mut_51 36 16 51 0 49 0 45 0 54 | Mut_52 34 9 48 0 51 0 43 1 55 | Mut_53 35 8 49 0 49 0 43 1 56 | Mut_54 41 15 33 0 49 0 56 0 57 | Mut_55 41 9 54 0 49 0 52 1 58 | Mut_56 38 3 52 0 52 0 47 0 59 | Mut_57 39 8 54 0 57 0 46 0 60 | Mut_58 47 6 48 0 59 0 67 0 61 | Mut_59 42 6 46 0 49 0 50 1 62 | Mut_60 38 10 44 0 50 0 46 0 63 | Mut_61 37 7 44 0 48 0 51 0 64 | Mut_62 31 9 43 0 52 0 57 0 65 | Mut_63 45 8 49 0 37 0 44 0 66 | Mut_64 51 5 55 0 57 0 43 2 67 | Mut_65 27 25 39 10 19 29 38 13 68 | Mut_66 34 31 35 10 28 27 34 19 69 | Mut_67 22 16 33 8 37 28 36 13 70 | Mut_68 26 23 38 15 22 27 37 9 71 | Mut_69 24 21 43 11 29 22 37 18 72 | Mut_70 26 22 38 7 28 23 27 19 73 | Mut_71 37 0 38 2 60 0 39 7 74 | Mut_72 49 0 42 3 44 0 38 8 75 | Mut_73 49 0 49 0 47 0 32 13 76 | Mut_74 45 0 55 0 60 0 46 9 77 | Mut_75 48 0 45 1 53 0 44 8 78 | Mut_76 28 24 42 8 46 8 32 3 79 | Mut_77 23 29 34 7 31 13 39 15 80 | Mut_78 28 28 45 6 37 9 54 15 81 | Mut_79 27 18 36 6 38 16 41 16 82 | Mut_80 21 25 29 9 39 9 34 9 83 | Mut_81 21 21 46 8 36 10 34 17 84 | Mut_82 18 24 28 4 23 10 37 17 85 | Mut_83 26 28 53 12 41 12 53 7 86 | Mut_84 24 28 54 6 34 7 41 17 87 | Mut_85 23 30 36 5 44 14 40 7 88 | Mut_86 34 25 37 11 38 11 39 14 89 | Mut_87 42 6 38 8 58 0 39 10 90 | Mut_88 48 8 43 6 54 0 50 13 91 | Mut_89 38 14 38 10 49 0 41 14 92 | Mut_90 49 11 38 6 48 0 43 15 93 | Mut_91 51 6 44 7 53 0 44 7 94 | Mut_92 52 3 36 6 36 0 36 12 95 | Mut_93 38 2 47 5 35 0 24 8 96 | Mut_94 42 7 38 7 45 0 27 11 97 | Mut_95 54 4 50 9 42 0 36 12 98 | Mut_96 41 7 39 7 58 0 44 12 99 | Mut_97 39 6 57 8 53 0 37 9 100 | Mut_98 46 9 44 3 50 0 37 11 101 | Mut_99 37 7 52 3 57 0 49 9 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_3.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 32 10 49 8 44 3 30 11 3 | Mut_1 26 14 37 14 32 6 26 11 4 | Mut_2 39 8 39 5 46 4 33 15 5 | Mut_3 51 1 59 0 55 0 45 0 6 | Mut_4 48 0 51 1 51 0 43 0 7 | Mut_5 40 2 42 3 61 0 33 0 8 | Mut_6 51 2 45 3 50 0 49 0 9 | Mut_7 58 3 51 2 46 0 40 0 10 | Mut_8 45 6 29 16 45 10 46 4 11 | Mut_9 37 9 37 15 45 6 55 1 12 | Mut_10 43 7 39 13 49 8 49 6 13 | Mut_11 59 15 49 21 42 8 49 4 14 | Mut_12 37 6 36 12 56 6 48 5 15 | Mut_13 48 3 39 12 36 7 43 1 16 | Mut_14 56 6 36 12 41 8 44 1 17 | Mut_15 42 9 39 11 35 10 44 4 18 | Mut_16 40 12 36 10 39 9 52 1 19 | Mut_17 43 5 40 12 45 6 54 5 20 | Mut_18 43 8 45 15 34 4 47 2 21 | Mut_19 44 14 29 19 39 9 54 1 22 | Mut_20 46 11 38 11 39 7 53 2 23 | Mut_21 38 6 43 12 41 11 51 2 24 | Mut_22 42 5 42 13 43 4 52 3 25 | Mut_23 43 7 37 13 44 5 45 1 26 | Mut_24 40 5 34 15 45 6 44 1 27 | Mut_25 56 5 33 17 52 17 52 0 28 | Mut_26 44 7 35 20 38 7 38 3 29 | Mut_27 56 8 23 13 29 11 55 3 30 | Mut_28 37 7 37 20 39 7 56 6 31 | Mut_29 55 8 33 18 47 3 49 3 32 | Mut_30 46 6 29 19 48 6 62 2 33 | Mut_31 46 8 29 14 43 12 39 2 34 | Mut_32 47 8 35 8 43 6 51 2 35 | Mut_33 56 2 47 3 49 0 43 0 36 | Mut_34 42 0 56 2 48 0 43 0 37 | Mut_35 55 2 47 0 47 0 55 0 38 | Mut_36 46 6 50 0 64 0 50 1 39 | Mut_37 51 2 51 0 50 0 49 0 40 | Mut_38 52 1 46 1 54 0 51 0 41 | Mut_39 25 24 28 20 37 15 33 18 42 | Mut_40 30 22 23 26 39 15 32 27 43 | Mut_41 30 18 27 23 34 16 30 15 44 | Mut_42 17 16 32 23 39 11 29 22 45 | Mut_43 22 25 35 20 31 21 37 21 46 | Mut_44 27 18 28 20 40 11 31 21 47 | Mut_45 39 22 27 31 39 12 23 13 48 | Mut_46 30 21 43 18 45 14 25 22 49 | Mut_47 27 23 23 28 46 12 34 18 50 | Mut_48 42 26 17 14 40 17 33 13 51 | Mut_49 32 25 26 20 36 9 31 18 52 | Mut_50 20 16 29 25 37 11 35 29 53 | Mut_51 24 21 18 33 36 15 26 16 54 | Mut_52 22 22 21 21 31 13 22 20 55 | Mut_53 20 24 33 23 39 12 21 16 56 | Mut_54 25 24 34 31 44 15 31 24 57 | Mut_55 26 23 24 26 39 15 31 26 58 | Mut_56 32 19 22 24 31 17 32 20 59 | Mut_57 22 26 27 15 40 13 41 20 60 | Mut_58 24 19 23 27 38 12 29 31 61 | Mut_59 34 17 31 26 42 24 30 26 62 | Mut_60 28 21 34 22 44 10 32 25 63 | Mut_61 51 3 52 1 49 0 58 1 64 | Mut_62 39 2 43 0 49 0 59 0 65 | Mut_63 49 2 44 0 40 0 48 0 66 | Mut_64 54 3 60 3 53 0 50 1 67 | Mut_65 37 3 54 1 43 0 42 0 68 | Mut_66 43 2 43 0 45 0 48 0 69 | Mut_67 49 2 52 0 52 0 50 0 70 | Mut_68 55 4 49 0 68 0 55 0 71 | Mut_69 58 1 48 1 57 0 59 0 72 | Mut_70 57 1 46 0 47 0 38 1 73 | Mut_71 54 0 56 0 43 0 38 0 74 | Mut_72 47 1 51 0 40 0 46 1 75 | Mut_73 54 3 61 2 59 0 65 2 76 | Mut_74 42 2 50 2 51 0 50 0 77 | Mut_75 45 2 59 1 54 0 56 0 78 | Mut_76 33 9 60 0 47 6 40 0 79 | Mut_77 56 1 50 0 42 7 53 1 80 | Mut_78 44 0 46 0 43 7 50 1 81 | Mut_79 34 0 48 0 47 7 33 3 82 | Mut_80 43 0 53 0 29 8 59 1 83 | Mut_81 49 0 46 0 45 7 36 2 84 | Mut_82 40 1 52 0 45 3 39 2 85 | Mut_83 38 0 42 0 42 2 47 2 86 | Mut_84 56 0 47 0 48 8 50 2 87 | Mut_85 53 1 55 0 45 6 50 4 88 | Mut_86 39 1 47 0 42 9 44 2 89 | Mut_87 47 0 43 0 35 4 53 4 90 | Mut_88 41 2 57 0 37 4 42 2 91 | Mut_89 41 2 46 0 39 6 38 6 92 | Mut_90 53 2 53 0 40 11 54 1 93 | Mut_91 42 4 39 3 55 0 65 0 94 | Mut_92 55 1 45 3 55 0 44 0 95 | Mut_93 49 0 62 3 51 0 50 0 96 | Mut_94 32 3 46 1 51 0 37 0 97 | Mut_95 43 0 39 0 62 0 50 0 98 | Mut_96 63 5 43 1 49 0 41 0 99 | Mut_97 41 2 45 1 63 0 51 0 100 | Mut_98 49 2 45 1 60 0 48 0 101 | Mut_99 45 1 40 1 53 0 60 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_1.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 29 11 69 8 33 20 32 18 3 | Mut_1 29 17 48 6 34 18 33 20 4 | Mut_2 29 15 44 2 32 15 36 16 5 | Mut_3 43 10 44 4 34 17 22 21 6 | Mut_4 35 16 41 3 23 14 26 27 7 | Mut_5 26 20 59 4 29 13 38 20 8 | Mut_6 31 9 55 3 31 17 26 20 9 | Mut_7 34 17 35 3 33 13 34 20 10 | Mut_8 30 13 34 2 42 20 24 23 11 | Mut_9 36 12 55 0 23 15 27 22 12 | Mut_10 31 7 42 4 35 14 31 26 13 | Mut_11 32 12 51 5 27 9 30 24 14 | Mut_12 28 7 50 5 26 12 26 29 15 | Mut_13 43 12 37 2 38 18 28 27 16 | Mut_14 35 13 41 4 37 16 31 16 17 | Mut_15 41 16 44 4 41 17 36 26 18 | Mut_16 32 18 35 7 33 14 25 18 19 | Mut_17 40 11 47 2 27 21 31 22 20 | Mut_18 41 19 53 5 27 9 29 23 21 | Mut_19 33 13 40 7 30 15 26 21 22 | Mut_20 25 14 40 7 34 14 39 25 23 | Mut_21 34 14 48 6 28 22 36 18 24 | Mut_22 30 13 47 2 31 26 30 15 25 | Mut_23 26 13 46 3 31 29 28 19 26 | Mut_24 39 13 35 2 29 11 36 21 27 | Mut_25 34 16 50 7 33 14 25 21 28 | Mut_26 44 23 51 6 38 16 27 23 29 | Mut_27 36 13 51 2 31 19 30 21 30 | Mut_28 36 10 48 4 33 15 26 26 31 | Mut_29 26 11 52 3 38 18 25 15 32 | Mut_30 36 16 44 4 29 20 23 18 33 | Mut_31 38 21 35 3 39 12 32 28 34 | Mut_32 47 4 52 1 53 0 23 20 35 | Mut_33 35 15 46 1 49 0 32 19 36 | Mut_34 39 6 42 1 52 0 36 19 37 | Mut_35 32 13 47 2 53 0 20 21 38 | Mut_36 26 11 53 0 47 0 31 16 39 | Mut_37 33 26 43 0 47 0 23 21 40 | Mut_38 29 13 41 0 55 0 27 12 41 | Mut_39 34 10 54 0 59 0 32 19 42 | Mut_40 34 17 50 0 40 0 26 20 43 | Mut_41 42 19 61 1 54 0 36 18 44 | Mut_42 33 15 61 3 49 0 28 17 45 | Mut_43 42 6 46 0 39 9 59 0 46 | Mut_44 40 11 42 0 42 5 51 0 47 | Mut_45 38 6 52 0 51 7 46 0 48 | Mut_46 37 8 38 0 50 13 54 0 49 | Mut_47 36 7 62 0 49 1 40 0 50 | Mut_48 32 9 51 0 35 7 57 0 51 | Mut_49 24 12 53 0 31 10 56 0 52 | Mut_50 50 10 51 0 40 9 48 0 53 | Mut_51 28 24 29 33 30 25 37 21 54 | Mut_52 31 6 61 1 37 0 51 0 55 | Mut_53 54 0 46 0 38 12 49 0 56 | Mut_54 57 2 47 0 54 0 24 21 57 | Mut_55 43 3 48 0 52 0 26 17 58 | Mut_56 61 4 54 0 43 0 30 29 59 | Mut_57 50 3 59 0 55 0 34 33 60 | Mut_58 54 3 64 0 52 0 24 17 61 | Mut_59 56 1 54 0 48 0 30 23 62 | Mut_60 46 2 40 0 55 0 24 17 63 | Mut_61 59 3 66 0 49 0 31 17 64 | Mut_62 45 2 49 0 42 0 31 20 65 | Mut_63 64 2 55 0 60 0 29 24 66 | Mut_64 46 0 28 15 47 0 46 0 67 | Mut_65 54 0 40 15 42 0 53 0 68 | Mut_66 36 0 39 22 45 0 64 0 69 | Mut_67 55 0 55 0 41 3 49 0 70 | Mut_68 43 0 41 1 59 7 49 0 71 | Mut_69 52 0 49 0 32 8 57 0 72 | Mut_70 51 0 42 0 53 8 51 0 73 | Mut_71 48 0 42 0 49 5 37 0 74 | Mut_72 57 0 47 2 44 12 61 0 75 | Mut_73 62 0 47 1 45 6 59 0 76 | Mut_74 47 0 55 0 46 7 55 0 77 | Mut_75 48 0 50 2 55 8 55 0 78 | Mut_76 44 0 43 0 43 6 49 0 79 | Mut_77 36 0 50 1 55 4 64 0 80 | Mut_78 41 0 39 1 41 9 52 0 81 | Mut_79 43 0 50 0 53 13 60 0 82 | Mut_80 61 0 58 0 44 5 53 0 83 | Mut_81 60 0 49 2 41 5 41 0 84 | Mut_82 50 0 48 0 45 11 40 0 85 | Mut_83 56 0 57 0 45 13 45 0 86 | Mut_84 51 0 42 0 40 5 62 0 87 | Mut_85 53 0 51 1 40 7 41 0 88 | Mut_86 47 0 72 0 40 8 54 0 89 | Mut_87 47 0 41 0 34 3 41 0 90 | Mut_88 40 0 45 1 36 8 35 0 91 | Mut_89 66 0 46 1 47 6 42 0 92 | Mut_90 47 0 39 0 38 10 64 0 93 | Mut_91 66 0 56 0 50 5 66 0 94 | Mut_92 56 0 65 0 43 10 55 0 95 | Mut_93 57 0 55 1 45 6 41 0 96 | Mut_94 55 0 48 4 33 12 51 0 97 | Mut_95 55 0 41 3 36 4 51 0 98 | Mut_96 49 0 45 2 39 2 67 0 99 | Mut_97 40 0 41 6 49 8 48 0 100 | Mut_98 44 0 48 0 46 6 56 0 101 | Mut_99 44 0 41 3 46 9 50 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_9.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 44 16 48 5 36 11 45 6 3 | Mut_1 36 10 39 4 48 8 37 2 4 | Mut_2 42 13 39 6 40 8 39 4 5 | Mut_3 42 17 52 6 42 12 59 1 6 | Mut_4 29 11 41 7 36 10 45 1 7 | Mut_5 44 11 39 8 41 9 44 5 8 | Mut_6 39 13 36 8 33 9 47 4 9 | Mut_7 45 11 44 2 43 9 56 10 10 | Mut_8 38 13 51 4 42 8 46 0 11 | Mut_9 42 10 41 9 27 13 54 4 12 | Mut_10 43 12 35 4 33 6 46 4 13 | Mut_11 31 12 46 8 52 0 47 0 14 | Mut_12 30 10 53 7 47 0 62 0 15 | Mut_13 42 11 43 6 49 0 54 0 16 | Mut_14 41 6 44 2 54 0 56 0 17 | Mut_15 39 8 43 4 49 0 55 0 18 | Mut_16 51 9 39 7 65 0 54 0 19 | Mut_17 52 7 41 5 46 0 44 0 20 | Mut_18 35 12 54 12 49 0 46 0 21 | Mut_19 34 9 34 4 39 0 50 0 22 | Mut_20 38 6 53 8 39 10 39 4 23 | Mut_21 42 10 38 5 40 10 40 4 24 | Mut_22 40 7 40 6 37 10 52 2 25 | Mut_23 40 9 48 8 37 8 48 6 26 | Mut_24 30 9 52 9 31 10 58 4 27 | Mut_25 46 11 47 3 37 8 43 3 28 | Mut_26 28 9 46 4 50 10 44 2 29 | Mut_27 37 10 47 11 33 12 45 5 30 | Mut_28 30 9 29 6 46 1 44 4 31 | Mut_29 38 10 40 8 37 11 56 3 32 | Mut_30 47 11 53 6 38 8 47 7 33 | Mut_31 31 12 34 4 35 9 48 2 34 | Mut_32 48 11 27 12 31 5 45 4 35 | Mut_33 37 12 37 5 36 9 55 5 36 | Mut_34 43 5 41 8 38 8 51 3 37 | Mut_35 44 6 41 6 47 14 59 3 38 | Mut_36 32 8 35 2 52 9 46 3 39 | Mut_37 45 11 45 7 36 11 53 2 40 | Mut_38 27 12 45 10 41 12 49 3 41 | Mut_39 55 8 37 8 39 6 43 5 42 | Mut_40 24 8 40 4 40 13 44 5 43 | Mut_41 46 11 41 9 34 12 58 3 44 | Mut_42 41 8 40 5 33 11 47 3 45 | Mut_43 38 12 45 7 30 7 43 3 46 | Mut_44 42 9 51 8 56 9 57 4 47 | Mut_45 46 13 42 9 32 14 42 3 48 | Mut_46 29 6 46 2 55 11 51 3 49 | Mut_47 52 0 57 0 37 9 41 2 50 | Mut_48 51 0 45 0 39 12 49 3 51 | Mut_49 37 0 46 0 38 16 58 7 52 | Mut_50 62 0 71 0 39 9 48 0 53 | Mut_51 39 0 51 0 50 7 50 3 54 | Mut_52 45 0 53 0 49 9 56 3 55 | Mut_53 56 0 42 0 32 10 47 1 56 | Mut_54 51 0 55 0 48 9 45 3 57 | Mut_55 56 0 50 0 39 11 39 1 58 | Mut_56 46 0 46 0 36 5 52 0 59 | Mut_57 61 0 45 0 36 9 52 1 60 | Mut_58 52 0 43 0 34 7 51 4 61 | Mut_59 50 0 45 0 32 6 52 1 62 | Mut_60 42 0 65 0 35 8 46 5 63 | Mut_61 52 0 42 0 43 7 49 5 64 | Mut_62 65 0 52 0 34 15 50 2 65 | Mut_63 50 0 52 1 48 6 47 1 66 | Mut_64 42 14 42 10 55 0 56 0 67 | Mut_65 45 12 49 4 50 0 57 0 68 | Mut_66 31 9 39 6 41 0 42 0 69 | Mut_67 37 11 51 9 54 0 52 0 70 | Mut_68 29 24 26 21 35 21 42 25 71 | Mut_69 25 17 36 20 30 23 22 30 72 | Mut_70 29 19 30 27 37 9 22 21 73 | Mut_71 37 19 31 24 36 16 28 16 74 | Mut_72 24 17 32 22 31 12 22 23 75 | Mut_73 29 19 34 21 31 15 24 25 76 | Mut_74 33 16 26 16 25 8 31 26 77 | Mut_75 32 15 21 23 23 11 23 26 78 | Mut_76 34 22 23 13 29 22 26 22 79 | Mut_77 35 27 30 22 30 21 23 24 80 | Mut_78 28 20 27 19 29 15 25 30 81 | Mut_79 31 16 27 21 32 17 26 23 82 | Mut_80 28 22 25 27 38 28 30 30 83 | Mut_81 24 17 35 21 30 18 21 31 84 | Mut_82 30 18 29 18 29 19 27 26 85 | Mut_83 30 19 18 23 41 17 27 27 86 | Mut_84 31 16 33 23 31 15 30 16 87 | Mut_85 40 24 36 19 32 13 23 27 88 | Mut_86 41 5 38 16 43 0 50 0 89 | Mut_87 39 6 52 12 58 0 47 0 90 | Mut_88 42 2 52 4 54 0 50 0 91 | Mut_89 47 8 42 15 67 0 46 0 92 | Mut_90 45 11 41 6 47 0 59 0 93 | Mut_91 45 5 43 11 55 0 59 0 94 | Mut_92 36 4 37 5 53 0 40 0 95 | Mut_93 40 6 36 10 47 0 54 0 96 | Mut_94 29 2 36 7 43 0 51 0 97 | Mut_95 42 10 51 8 56 0 56 0 98 | Mut_96 48 1 22 5 65 0 50 0 99 | Mut_97 37 11 44 8 50 12 56 5 100 | Mut_98 30 16 21 12 30 15 23 29 101 | Mut_99 30 17 33 12 33 12 33 19 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_0.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 52 0 46 8 46 0 48 0 3 | Mut_1 47 0 49 6 44 0 41 0 4 | Mut_2 63 0 31 8 44 0 43 0 5 | Mut_3 53 0 39 8 55 0 50 0 6 | Mut_4 45 0 36 5 40 1 59 0 7 | Mut_5 49 0 35 8 55 1 50 0 8 | Mut_6 48 0 44 9 39 0 48 0 9 | Mut_7 44 0 39 4 45 0 55 0 10 | Mut_8 34 0 42 12 47 0 51 0 11 | Mut_9 52 0 45 5 54 0 55 0 12 | Mut_10 48 0 39 7 67 0 51 0 13 | Mut_11 32 10 36 5 42 9 55 0 14 | Mut_12 37 9 40 11 50 8 56 0 15 | Mut_13 41 5 34 10 40 11 47 0 16 | Mut_14 42 8 41 22 51 10 51 0 17 | Mut_15 43 12 38 11 40 11 44 0 18 | Mut_16 31 5 44 14 42 12 42 0 19 | Mut_17 39 3 40 14 40 4 48 0 20 | Mut_18 42 6 34 13 35 4 48 0 21 | Mut_19 34 8 32 9 41 7 49 0 22 | Mut_20 38 8 44 11 32 8 37 0 23 | Mut_21 46 10 46 9 53 4 62 0 24 | Mut_22 41 6 32 8 65 0 48 0 25 | Mut_23 39 2 41 11 48 0 39 0 26 | Mut_24 45 9 42 11 56 0 36 0 27 | Mut_25 47 4 38 7 54 0 56 0 28 | Mut_26 36 4 39 8 61 0 52 0 29 | Mut_27 41 11 37 7 66 0 56 0 30 | Mut_28 48 6 35 6 42 0 53 0 31 | Mut_29 42 4 45 7 55 0 46 0 32 | Mut_30 44 7 37 13 63 0 74 0 33 | Mut_31 42 5 25 13 53 0 55 0 34 | Mut_32 47 10 45 9 47 0 52 0 35 | Mut_33 49 8 46 11 59 0 54 0 36 | Mut_34 40 5 39 11 48 0 48 0 37 | Mut_35 46 5 33 10 66 0 42 0 38 | Mut_36 34 11 48 6 46 0 52 0 39 | Mut_37 37 6 47 11 59 0 50 0 40 | Mut_38 29 10 50 8 46 0 55 0 41 | Mut_39 51 6 36 14 50 0 57 0 42 | Mut_40 36 4 41 5 51 0 49 0 43 | Mut_41 46 4 39 7 51 0 51 0 44 | Mut_42 48 5 50 11 49 0 44 0 45 | Mut_43 38 8 44 2 49 0 55 0 46 | Mut_44 46 8 40 9 52 0 53 0 47 | Mut_45 46 5 48 8 55 0 39 0 48 | Mut_46 50 12 45 11 46 0 39 0 49 | Mut_47 37 6 37 8 50 0 39 0 50 | Mut_48 33 8 45 14 64 0 50 0 51 | Mut_49 55 5 43 9 45 1 51 0 52 | Mut_50 42 2 45 4 45 0 57 0 53 | Mut_51 47 1 42 8 62 1 56 0 54 | Mut_52 42 2 48 10 51 1 31 0 55 | Mut_53 51 2 40 7 49 1 47 0 56 | Mut_54 44 0 30 8 44 0 44 0 57 | Mut_55 35 21 41 0 43 14 44 11 58 | Mut_56 33 17 52 0 40 11 48 9 59 | Mut_57 32 19 23 24 33 17 39 7 60 | Mut_58 25 25 27 17 27 29 38 8 61 | Mut_59 28 24 21 20 27 26 33 8 62 | Mut_60 29 31 36 13 27 35 31 13 63 | Mut_61 17 26 27 18 30 13 41 9 64 | Mut_62 27 23 19 25 23 23 49 11 65 | Mut_63 23 24 39 16 29 23 36 8 66 | Mut_64 25 24 30 21 21 22 31 8 67 | Mut_65 22 23 25 13 21 18 51 11 68 | Mut_66 23 21 27 15 26 21 38 6 69 | Mut_67 27 23 39 20 28 15 33 9 70 | Mut_68 38 24 28 27 36 19 36 12 71 | Mut_69 30 22 38 16 27 23 44 12 72 | Mut_70 28 21 27 21 27 29 39 4 73 | Mut_71 34 30 25 23 27 15 34 6 74 | Mut_72 29 21 26 10 28 25 43 11 75 | Mut_73 24 21 27 19 29 24 40 9 76 | Mut_74 24 25 38 13 39 24 52 11 77 | Mut_75 19 24 30 22 29 20 45 13 78 | Mut_76 31 33 20 19 28 20 42 15 79 | Mut_77 26 22 23 23 31 22 40 13 80 | Mut_78 18 28 26 15 26 18 33 9 81 | Mut_79 26 22 36 11 33 24 37 9 82 | Mut_80 20 26 39 17 30 20 30 10 83 | Mut_81 26 17 37 12 26 14 44 7 84 | Mut_82 29 19 36 23 20 27 39 8 85 | Mut_83 28 22 19 28 22 21 38 4 86 | Mut_84 35 16 35 15 32 16 46 8 87 | Mut_85 26 29 34 22 27 19 36 11 88 | Mut_86 24 18 38 12 34 25 39 8 89 | Mut_87 25 22 35 21 18 27 46 6 90 | Mut_88 36 15 47 0 37 18 55 0 91 | Mut_89 29 16 49 0 35 12 60 0 92 | Mut_90 37 14 47 0 47 22 55 0 93 | Mut_91 53 0 49 0 55 3 47 0 94 | Mut_92 51 0 52 2 53 5 46 0 95 | Mut_93 43 0 42 0 40 1 52 0 96 | Mut_94 47 3 52 0 47 4 54 0 97 | Mut_95 42 1 44 0 45 4 48 0 98 | Mut_96 56 0 51 0 52 7 47 0 99 | Mut_97 56 0 52 2 49 7 65 0 100 | Mut_98 47 0 45 1 49 5 39 0 101 | Mut_99 38 0 52 1 46 7 43 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_2.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 37 7 41 10 51 0 50 0 3 | Mut_1 37 9 27 9 61 0 42 0 4 | Mut_2 37 8 46 10 52 0 50 0 5 | Mut_3 43 17 35 6 56 0 58 0 6 | Mut_4 42 12 51 5 55 0 53 0 7 | Mut_5 41 11 56 9 45 0 52 0 8 | Mut_6 43 13 48 9 50 0 47 0 9 | Mut_7 32 8 41 7 43 0 48 0 10 | Mut_8 33 13 47 6 48 0 54 0 11 | Mut_9 34 8 48 3 48 0 58 0 12 | Mut_10 34 15 36 10 62 0 35 0 13 | Mut_11 33 9 39 9 59 0 50 0 14 | Mut_12 35 13 24 8 52 0 44 0 15 | Mut_13 24 12 42 8 45 0 43 0 16 | Mut_14 28 16 43 11 58 0 52 0 17 | Mut_15 52 5 29 15 64 0 46 0 18 | Mut_16 33 11 52 9 46 0 45 0 19 | Mut_17 53 8 35 12 49 0 42 0 20 | Mut_18 34 14 43 6 48 0 41 0 21 | Mut_19 39 8 44 6 49 0 45 0 22 | Mut_20 28 18 34 7 72 0 55 0 23 | Mut_21 39 13 49 10 49 0 55 0 24 | Mut_22 47 6 46 5 43 0 46 0 25 | Mut_23 37 12 42 7 55 0 57 0 26 | Mut_24 32 11 43 15 61 0 39 0 27 | Mut_25 42 9 48 12 67 0 44 0 28 | Mut_26 33 8 42 7 52 0 50 0 29 | Mut_27 48 0 65 0 62 0 41 1 30 | Mut_28 60 0 49 0 56 0 53 1 31 | Mut_29 41 1 44 0 46 0 54 0 32 | Mut_30 42 16 44 0 37 19 51 0 33 | Mut_31 35 13 47 0 32 19 44 0 34 | Mut_32 33 8 31 0 24 18 61 0 35 | Mut_33 41 8 47 0 37 15 54 0 36 | Mut_34 26 9 36 0 35 13 50 0 37 | Mut_35 26 18 29 22 29 19 24 34 38 | Mut_36 32 24 27 19 20 20 28 22 39 | Mut_37 23 26 27 25 36 20 26 23 40 | Mut_38 22 11 24 18 28 26 26 24 41 | Mut_39 28 25 26 16 38 26 23 27 42 | Mut_40 28 26 25 35 35 21 27 25 43 | Mut_41 27 18 27 30 28 14 30 19 44 | Mut_42 32 22 29 22 24 20 29 29 45 | Mut_43 24 24 26 27 23 14 29 28 46 | Mut_44 26 21 23 18 32 23 23 21 47 | Mut_45 33 16 30 29 34 19 30 17 48 | Mut_46 28 25 37 26 25 18 25 27 49 | Mut_47 25 18 27 20 42 27 25 25 50 | Mut_48 30 21 19 27 21 15 23 16 51 | Mut_49 23 19 25 28 27 22 30 27 52 | Mut_50 23 25 21 30 30 18 22 28 53 | Mut_51 21 19 25 24 33 24 23 24 54 | Mut_52 30 26 22 24 19 22 17 30 55 | Mut_53 28 28 32 21 28 19 23 29 56 | Mut_54 28 24 30 19 30 25 27 36 57 | Mut_55 32 21 25 16 38 12 21 27 58 | Mut_56 53 13 45 0 27 17 50 0 59 | Mut_57 51 0 47 3 52 0 38 13 60 | Mut_58 52 0 35 10 47 4 51 0 61 | Mut_59 55 0 43 15 50 1 63 0 62 | Mut_60 46 0 34 10 43 1 48 0 63 | Mut_61 42 0 46 23 55 2 33 0 64 | Mut_62 51 0 43 12 46 1 60 0 65 | Mut_63 49 0 37 11 45 0 49 0 66 | Mut_64 42 0 28 18 48 2 60 0 67 | Mut_65 37 0 37 18 40 0 49 0 68 | Mut_66 48 0 32 9 49 0 51 0 69 | Mut_67 63 0 37 14 51 1 60 0 70 | Mut_68 46 0 40 10 46 4 40 0 71 | Mut_69 48 0 43 11 54 1 45 0 72 | Mut_70 55 0 46 9 51 3 51 0 73 | Mut_71 55 0 51 10 41 3 53 0 74 | Mut_72 48 0 31 11 51 2 57 0 75 | Mut_73 56 0 37 14 38 2 55 0 76 | Mut_74 47 0 32 14 43 1 32 0 77 | Mut_75 44 0 50 11 42 1 43 0 78 | Mut_76 48 0 43 8 53 5 57 0 79 | Mut_77 51 0 40 11 51 4 58 0 80 | Mut_78 54 0 40 18 55 1 40 0 81 | Mut_79 61 0 38 16 54 1 56 0 82 | Mut_80 60 0 34 13 54 2 37 0 83 | Mut_81 61 0 44 11 51 1 49 0 84 | Mut_82 49 0 24 14 44 3 49 0 85 | Mut_83 45 0 47 14 48 3 43 0 86 | Mut_84 52 0 33 13 44 0 46 0 87 | Mut_85 49 0 43 12 52 0 50 0 88 | Mut_86 52 0 43 10 44 1 45 0 89 | Mut_87 61 0 29 9 61 5 40 0 90 | Mut_88 63 0 41 13 46 0 42 0 91 | Mut_89 52 0 26 12 47 1 54 0 92 | Mut_90 55 0 39 15 48 2 62 0 93 | Mut_91 47 0 34 23 59 4 42 0 94 | Mut_92 56 0 53 0 36 0 45 7 95 | Mut_93 49 0 50 0 54 0 44 5 96 | Mut_94 55 0 46 1 47 0 39 7 97 | Mut_95 52 0 48 2 36 0 27 8 98 | Mut_96 56 0 53 1 55 0 31 6 99 | Mut_97 46 0 52 0 50 0 47 3 100 | Mut_98 31 7 51 1 28 25 23 18 101 | Mut_99 42 12 54 4 40 12 33 18 102 | -------------------------------------------------------------------------------- /data/real/EV003.txt: -------------------------------------------------------------------------------- 1 | gene_id R9 R9 R6 R6 R5 R5 R2 R2 R4 R4 R3 R3 R1 R1 R7 R7 2 | LAMC1,chr1:183091353 808 831 1215 357 1414 292 1022 268 1030 317 977 345 544 178 1198 381 3 | ZNF238,chr1:244217624 804 264 1214 139 848 210 623 188 573 174 648 182 519 141 795 210 4 | HADHB,chr2:26502887 607 373 980 132 884 280 906 281 909 261 827 260 577 150 837 258 5 | PTCD3,chr2:86348641 645 382 996 140 1121 286 928 265 854 284 910 308 569 183 808 248 6 | PBRM1,chr3:52643360 248 380 894 152 890 314 679 312 617 297 594 328 324 164 669 314 7 | UGT2A,chr4:70455148 513 270 871 137 767 179 707 205 635 208 628 222 554 150 612 190 8 | ALB,chr4:74284020 697 372 1329 216 1430 282 897 253 822 284 897 326 566 195 1004 341 9 | PURA,chr5:139494232 674 55 853 133 1185 229 761 163 717 170 724 194 556 128 866 211 10 | ZBTB5,chr9:37441083 689 378 1227 165 1289 377 935 292 964 293 983 338 728 222 1150 337 11 | DAK,chr11:61112943 476 303 873 139 875 290 696 234 676 205 688 258 511 170 776 274 12 | DGAT2,chr11:75508233 785 405 1157 149 1175 298 1001 300 1018 282 894 295 639 227 1048 353 13 | CWF19L2,chr11:107300158 379 233 714 95 726 146 681 165 630 219 551 205 329 123 527 175 14 | GRIK4,chr11:120827623 575 228 990 100 983 140 773 143 728 159 705 179 555 143 746 170 15 | MNAT1,chr14:61201593 405 208 636 82 733 200 507 146 559 140 580 178 360 92 646 183 16 | SIPA1L1,chr14:72176168 485 280 753 113 874 206 672 180 589 208 560 214 391 112 770 245 17 | GOLGA5,chr14:93286100 749 364 1472 260 1836 459 1003 289 1093 283 930 291 588 141 1255 390 18 | MYST2,chr17:47874274 521 206 844 93 858 191 763 202 756 151 753 186 517 120 722 177 19 | CACTIN,chr19:3614474 538 273 881 125 1081 284 740 186 656 237 677 196 431 155 810 241 20 | RBL1,chr20:35651180 569 303 798 116 920 209 842 229 884 298 929 316 449 143 780 237 21 | KRTAP26-1,chr21:31692088 556 370 1099 194 1056 302 757 207 692 221 622 248 569 177 867 293 22 | KRTAP22-2,chr21:31962602 652 359 1243 203 1237 343 958 301 894 299 895 305 630 181 1006 296 23 | KBTBD8,chr3:67058726 245 105 348 65 545 3 367 0 423 0 317 0 176 0 386 0 24 | LONRF2,chr2:100910744 593 294 972 146 1397 0 1156 0 1043 0 1088 0 786 0 1150 0 25 | BHLHE40,chr3:5021701 224 273 674 127 884 0 697 0 699 0 717 0 475 0 779 0 26 | CMYA5,chr5:79027367 718 65 1208 172 1561 0 1243 0 1150 0 1114 0 800 0 1196 0 27 | GCC1,chr7:127222277 639 320 1081 120 1563 0 1376 0 1254 0 1268 0 882 0 1359 0 28 | SLC5A12,chr11:26743135 571 339 1100 175 1347 0 1111 0 999 0 979 0 741 0 1162 0 29 | YLPM1,chr14:75248260 795 470 1277 198 1578 0 1293 0 1323 0 1341 0 893 0 1363 0 30 | UTP14A,chrX:129058932 687 0 1209 135 1525 52 1073 12 1085 0 1202 0 614 0 1321 0 31 | MUC12,chr7:100648350 687 0 822 0 847 205 746 178 829 8 923 0 547 0 907 0 32 | C9orf79,chr9:90501800 613 0 1003 0 1028 191 831 192 1005 9 954 0 676 0 1112 0 33 | SAMD9L,chr7:92764111 880 0 1154 0 1128 238 814 208 943 0 969 0 606 0 1122 0 34 | PANK1,chr10:91359222 1104 0 1635 0 1454 274 997 232 1234 0 1276 0 705 0 1694 0 35 | IL16,chr15:81582809 747 377 1604 0 2052 0 1243 0 1159 0 1211 0 777 0 1661 0 36 | TTC14,chr3:180324050 889 0 1014 110 1327 0 1048 0 1086 0 916 0 603 0 1090 0 37 | ZFP64,chr20:50715012 925 0 989 0 1276 0 1208 0 1015 62 913 235 718 0 1121 0 38 | ZNF41,chrX:47308115 499 0 1191 0 1423 0 942 0 905 0 1023 0 497 52 1177 0 39 | C10orf18,chr10:5791986 981 0 1187 0 1423 0 1147 0 1139 0 1092 0 691 12 782 157 40 | MAST2,chr1:46471986 922 0 1216 0 1251 0 991 0 973 0 1112 0 694 0 831 259 41 | PPP1R7,chr2:242099869 911 0 1123 0 1381 0 1091 0 1175 0 1286 0 671 0 926 262 42 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_4.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 39 15 42 0 42 12 40 0 3 | Mut_1 25 12 51 0 49 8 41 0 4 | Mut_2 26 12 56 0 27 12 52 0 5 | Mut_3 38 15 34 1 42 8 42 0 6 | Mut_4 35 10 62 0 37 6 54 0 7 | Mut_5 41 11 56 1 53 7 57 0 8 | Mut_6 46 15 48 0 42 9 45 0 9 | Mut_7 33 15 40 0 37 7 48 0 10 | Mut_8 35 11 41 1 50 9 46 0 11 | Mut_9 35 15 60 0 37 10 50 0 12 | Mut_10 39 15 50 0 46 10 51 0 13 | Mut_11 50 8 38 3 38 0 47 0 14 | Mut_12 55 0 50 0 60 0 36 11 15 | Mut_13 46 2 15 21 48 2 49 3 16 | Mut_14 44 0 38 27 44 0 52 6 17 | Mut_15 59 0 24 24 54 0 50 0 18 | Mut_16 55 5 21 20 43 1 55 4 19 | Mut_17 40 4 25 20 49 1 42 7 20 | Mut_18 45 1 34 27 53 1 39 2 21 | Mut_19 34 0 36 22 54 1 44 6 22 | Mut_20 51 2 32 28 54 0 33 5 23 | Mut_21 43 6 26 22 55 3 36 6 24 | Mut_22 49 1 28 17 61 2 33 5 25 | Mut_23 42 4 23 18 45 2 58 7 26 | Mut_24 49 4 25 22 53 5 56 4 27 | Mut_25 57 2 24 26 36 2 37 4 28 | Mut_26 36 4 29 26 37 1 39 3 29 | Mut_27 53 1 26 23 47 2 42 11 30 | Mut_28 50 2 35 28 49 0 46 7 31 | Mut_29 41 1 35 20 34 2 46 6 32 | Mut_30 44 5 26 23 48 1 38 3 33 | Mut_31 49 1 24 26 49 1 44 4 34 | Mut_32 41 2 30 33 51 2 38 4 35 | Mut_33 56 0 29 20 47 3 42 4 36 | Mut_34 55 0 39 20 57 1 49 6 37 | Mut_35 44 0 32 22 44 1 50 0 38 | Mut_36 58 2 28 16 45 1 55 0 39 | Mut_37 49 3 26 15 46 3 44 0 40 | Mut_38 46 1 23 30 50 0 51 0 41 | Mut_39 56 0 30 16 51 2 43 0 42 | Mut_40 40 0 25 26 42 1 56 0 43 | Mut_41 45 1 21 21 56 2 45 0 44 | Mut_42 55 1 30 23 46 1 58 0 45 | Mut_43 55 4 27 20 45 3 48 0 46 | Mut_44 48 3 29 22 51 1 53 0 47 | Mut_45 53 2 31 27 38 2 43 0 48 | Mut_46 50 1 33 26 55 5 50 0 49 | Mut_47 39 2 31 22 53 0 44 0 50 | Mut_48 36 2 34 25 42 3 58 0 51 | Mut_49 48 1 27 25 41 0 63 0 52 | Mut_50 36 4 26 28 38 0 50 0 53 | Mut_51 47 1 19 18 53 0 47 0 54 | Mut_52 60 0 26 19 41 1 50 0 55 | Mut_53 41 0 21 29 44 2 46 0 56 | Mut_54 40 1 34 18 38 2 46 0 57 | Mut_55 40 0 30 21 45 2 63 0 58 | Mut_56 46 0 29 26 41 1 49 0 59 | Mut_57 57 4 33 21 31 0 35 0 60 | Mut_58 40 1 19 21 45 2 51 0 61 | Mut_59 61 2 25 21 51 1 51 0 62 | Mut_60 60 4 19 17 50 0 48 0 63 | Mut_61 51 0 40 19 57 3 49 0 64 | Mut_62 57 3 27 22 50 0 45 0 65 | Mut_63 42 1 26 21 64 1 42 0 66 | Mut_64 47 0 24 31 43 2 54 0 67 | Mut_65 49 5 27 26 59 1 60 0 68 | Mut_66 39 2 30 22 58 1 46 0 69 | Mut_67 45 0 42 22 50 2 46 0 70 | Mut_68 54 0 27 22 47 1 54 0 71 | Mut_69 55 1 28 21 51 1 49 0 72 | Mut_70 45 2 34 27 39 1 58 0 73 | Mut_71 29 29 33 29 27 15 40 20 74 | Mut_72 33 27 25 17 38 8 29 10 75 | Mut_73 20 22 22 22 37 13 29 13 76 | Mut_74 32 21 28 19 35 18 29 21 77 | Mut_75 30 14 19 24 34 18 33 19 78 | Mut_76 24 27 20 17 41 19 31 21 79 | Mut_77 29 31 20 29 39 15 41 19 80 | Mut_78 24 26 23 27 37 16 29 20 81 | Mut_79 22 20 19 18 46 17 35 16 82 | Mut_80 20 21 22 25 37 15 25 21 83 | Mut_81 38 18 26 30 46 17 30 16 84 | Mut_82 20 25 20 31 37 14 28 16 85 | Mut_83 27 22 30 18 31 19 30 20 86 | Mut_84 29 26 23 36 36 17 37 14 87 | Mut_85 25 28 28 22 35 20 26 14 88 | Mut_86 26 20 26 28 37 8 34 22 89 | Mut_87 21 20 31 26 41 22 42 17 90 | Mut_88 28 19 25 29 42 25 40 19 91 | Mut_89 33 19 14 31 42 14 38 26 92 | Mut_90 13 22 33 2 36 8 45 0 93 | Mut_91 22 20 39 0 25 16 61 0 94 | Mut_92 31 27 43 4 37 8 51 0 95 | Mut_93 34 0 60 0 41 5 40 12 96 | Mut_94 57 0 67 0 46 6 37 12 97 | Mut_95 48 0 56 0 48 8 53 8 98 | Mut_96 49 1 53 1 45 12 46 0 99 | Mut_97 38 15 45 1 40 10 47 0 100 | Mut_98 42 6 54 2 32 6 50 0 101 | Mut_99 31 9 52 1 39 8 52 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_7.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 57 1 55 7 33 19 52 7 3 | Mut_1 46 0 42 14 28 19 50 6 4 | Mut_2 41 0 42 10 37 16 51 7 5 | Mut_3 51 1 38 8 31 8 28 4 6 | Mut_4 49 0 46 6 29 15 40 4 7 | Mut_5 48 0 46 10 27 13 55 9 8 | Mut_6 33 1 41 6 30 16 28 2 9 | Mut_7 48 0 47 10 36 15 55 3 10 | Mut_8 54 1 36 5 28 19 38 9 11 | Mut_9 48 1 39 10 39 16 58 0 12 | Mut_10 53 0 51 0 58 0 46 6 13 | Mut_11 51 0 62 0 56 0 53 6 14 | Mut_12 40 0 52 0 52 0 45 4 15 | Mut_13 48 0 59 1 57 0 41 6 16 | Mut_14 55 0 40 0 54 0 43 8 17 | Mut_15 33 0 55 0 40 0 43 5 18 | Mut_16 52 0 49 0 45 0 46 11 19 | Mut_17 48 0 53 0 46 0 39 2 20 | Mut_18 47 0 46 0 35 0 33 6 21 | Mut_19 65 0 55 0 43 0 55 2 22 | Mut_20 53 0 51 0 47 0 39 1 23 | Mut_21 44 0 47 0 51 0 48 8 24 | Mut_22 37 0 42 0 46 0 44 5 25 | Mut_23 33 0 48 0 47 0 45 6 26 | Mut_24 43 0 44 0 51 0 45 2 27 | Mut_25 45 0 48 0 55 0 45 5 28 | Mut_26 42 0 46 0 45 0 42 3 29 | Mut_27 59 0 47 0 58 0 43 5 30 | Mut_28 45 0 55 0 39 0 43 5 31 | Mut_29 56 0 45 0 51 0 44 5 32 | Mut_30 51 0 44 0 57 0 36 4 33 | Mut_31 50 0 56 0 55 0 48 2 34 | Mut_32 61 3 56 0 38 8 47 0 35 | Mut_33 32 3 45 0 36 7 36 0 36 | Mut_34 40 5 45 0 38 10 40 0 37 | Mut_35 52 3 39 0 39 14 40 0 38 | Mut_36 52 0 41 8 56 0 51 0 39 | Mut_37 67 0 37 10 42 0 55 0 40 | Mut_38 50 0 41 14 42 0 50 0 41 | Mut_39 44 0 45 3 58 0 48 0 42 | Mut_40 45 0 44 14 51 0 46 0 43 | Mut_41 51 0 37 9 59 0 44 0 44 | Mut_42 53 0 31 22 51 0 53 0 45 | Mut_43 42 4 46 0 33 12 42 0 46 | Mut_44 63 6 56 0 36 17 46 0 47 | Mut_45 49 2 45 0 34 10 51 0 48 | Mut_46 53 5 45 0 38 13 44 0 49 | Mut_47 45 3 43 0 31 8 55 0 50 | Mut_48 48 2 48 0 46 7 53 0 51 | Mut_49 54 1 51 0 32 17 37 0 52 | Mut_50 36 2 52 0 52 16 60 0 53 | Mut_51 41 5 37 0 38 8 60 0 54 | Mut_52 41 7 54 0 44 10 40 0 55 | Mut_53 51 7 55 0 44 7 46 0 56 | Mut_54 41 2 45 0 45 12 53 0 57 | Mut_55 50 6 50 0 42 6 45 0 58 | Mut_56 47 3 32 0 35 8 48 0 59 | Mut_57 52 3 41 0 49 6 43 0 60 | Mut_58 39 3 48 0 35 12 50 0 61 | Mut_59 46 4 46 0 46 11 59 0 62 | Mut_60 26 21 27 14 22 28 32 19 63 | Mut_61 25 28 29 27 21 23 19 11 64 | Mut_62 22 23 20 15 30 29 29 11 65 | Mut_63 21 24 21 18 23 25 35 28 66 | Mut_64 33 31 41 18 23 18 27 18 67 | Mut_65 25 25 33 25 33 28 47 10 68 | Mut_66 28 21 25 19 22 29 38 16 69 | Mut_67 38 22 37 33 23 31 26 13 70 | Mut_68 25 17 24 21 27 21 27 22 71 | Mut_69 23 27 21 22 23 24 39 13 72 | Mut_70 29 22 34 25 18 25 33 18 73 | Mut_71 15 23 32 20 29 17 35 19 74 | Mut_72 22 14 25 11 27 25 36 16 75 | Mut_73 17 25 32 17 28 23 30 20 76 | Mut_74 25 19 25 25 23 23 26 21 77 | Mut_75 39 32 36 19 29 29 29 15 78 | Mut_76 31 24 27 20 25 32 37 17 79 | Mut_77 26 30 32 28 30 25 27 16 80 | Mut_78 27 24 30 15 19 24 38 17 81 | Mut_79 27 25 24 31 31 20 37 12 82 | Mut_80 23 21 36 19 15 19 36 16 83 | Mut_81 37 23 23 23 23 20 43 23 84 | Mut_82 20 28 24 20 16 15 31 11 85 | Mut_83 31 25 34 22 27 11 30 16 86 | Mut_84 30 22 25 18 21 16 31 17 87 | Mut_85 18 15 24 30 26 19 36 10 88 | Mut_86 62 0 39 9 39 19 45 0 89 | Mut_87 54 0 42 10 33 14 51 0 90 | Mut_88 53 0 39 10 36 25 46 0 91 | Mut_89 41 0 40 12 40 17 46 0 92 | Mut_90 44 0 50 8 38 18 48 0 93 | Mut_91 57 0 50 6 32 16 38 0 94 | Mut_92 45 0 40 9 26 20 53 0 95 | Mut_93 38 0 57 12 47 11 41 0 96 | Mut_94 52 0 46 10 36 11 50 0 97 | Mut_95 46 0 46 6 42 16 49 0 98 | Mut_96 31 12 54 5 48 0 53 0 99 | Mut_97 35 7 28 16 27 24 42 7 100 | Mut_98 55 11 41 15 26 23 58 2 101 | Mut_99 40 12 35 16 19 18 41 7 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_6.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 113 0 83 8 106 7 70 38 3 | Mut_1 119 0 80 10 100 6 71 29 4 | Mut_2 88 2 93 0 92 0 90 3 5 | Mut_3 86 3 86 0 116 0 107 3 6 | Mut_4 96 5 89 0 82 0 105 0 7 | Mut_5 99 6 92 0 100 0 98 0 8 | Mut_6 86 2 101 0 86 0 110 3 9 | Mut_7 90 7 97 0 101 0 94 0 10 | Mut_8 77 2 111 0 106 0 93 1 11 | Mut_9 81 3 112 0 92 0 111 0 12 | Mut_10 92 7 101 0 87 0 115 0 13 | Mut_11 115 5 106 0 91 0 89 3 14 | Mut_12 94 4 107 0 111 0 120 4 15 | Mut_13 85 4 108 0 88 0 93 1 16 | Mut_14 96 4 89 0 90 0 99 1 17 | Mut_15 105 0 83 0 96 0 108 4 18 | Mut_16 85 5 124 0 104 0 70 2 19 | Mut_17 95 5 96 0 108 0 97 1 20 | Mut_18 104 2 108 0 96 0 118 0 21 | Mut_19 97 3 95 0 113 0 86 2 22 | Mut_20 98 2 107 0 102 0 101 3 23 | Mut_21 97 8 116 0 91 0 121 1 24 | Mut_22 107 4 104 0 100 0 93 2 25 | Mut_23 102 5 110 0 101 0 114 1 26 | Mut_24 83 3 106 0 122 0 94 4 27 | Mut_25 72 3 99 0 80 0 88 2 28 | Mut_26 77 4 119 0 116 0 111 4 29 | Mut_27 89 3 103 0 93 0 91 0 30 | Mut_28 112 1 91 0 97 0 115 1 31 | Mut_29 99 3 113 0 87 0 95 2 32 | Mut_30 97 2 125 0 92 0 100 3 33 | Mut_31 86 2 94 0 104 0 92 1 34 | Mut_32 92 2 95 0 83 0 89 1 35 | Mut_33 93 2 88 0 86 0 95 1 36 | Mut_34 89 2 92 0 91 0 89 2 37 | Mut_35 94 5 98 0 84 0 101 0 38 | Mut_36 93 3 88 0 88 0 106 0 39 | Mut_37 84 4 92 0 110 0 105 1 40 | Mut_38 117 0 83 0 97 0 98 3 41 | Mut_39 92 2 128 0 96 0 94 1 42 | Mut_40 97 4 95 0 103 0 90 0 43 | Mut_41 86 2 94 0 96 0 100 3 44 | Mut_42 91 6 109 0 104 0 87 2 45 | Mut_43 104 7 96 0 95 0 109 2 46 | Mut_44 86 4 100 0 104 0 97 0 47 | Mut_45 103 3 103 0 98 0 109 2 48 | Mut_46 93 5 72 35 95 5 64 52 49 | Mut_47 105 4 68 42 94 5 49 41 50 | Mut_48 102 2 70 37 104 4 57 39 51 | Mut_49 94 2 66 43 103 6 63 44 52 | Mut_50 96 6 60 38 100 6 58 38 53 | Mut_51 100 3 70 31 90 8 62 45 54 | Mut_52 95 5 64 43 104 4 58 39 55 | Mut_53 119 6 62 33 94 2 55 48 56 | Mut_54 99 5 62 24 83 4 51 50 57 | Mut_55 104 3 68 31 80 5 66 40 58 | Mut_56 100 5 56 36 110 9 70 40 59 | Mut_57 94 3 64 37 89 4 80 33 60 | Mut_58 91 5 55 29 106 5 79 49 61 | Mut_59 97 7 73 35 91 7 54 30 62 | Mut_60 117 4 53 37 95 6 51 40 63 | Mut_61 110 6 84 24 95 0 109 0 64 | Mut_62 93 4 80 19 101 0 116 0 65 | Mut_63 49 50 58 41 82 26 58 39 66 | Mut_64 61 51 62 40 86 19 65 45 67 | Mut_65 53 34 61 38 65 30 62 37 68 | Mut_66 55 47 45 46 82 31 59 34 69 | Mut_67 58 45 51 34 86 29 68 40 70 | Mut_68 61 47 54 42 86 24 62 31 71 | Mut_69 59 57 49 53 80 27 64 40 72 | Mut_70 58 42 64 33 73 31 64 40 73 | Mut_71 57 50 54 43 72 33 52 31 74 | Mut_72 48 49 74 42 77 39 62 38 75 | Mut_73 50 41 58 38 79 21 58 32 76 | Mut_74 62 44 46 29 59 25 71 43 77 | Mut_75 57 51 63 28 82 17 70 25 78 | Mut_76 54 34 63 35 69 31 65 40 79 | Mut_77 64 51 61 35 92 23 54 51 80 | Mut_78 94 0 80 6 70 25 96 0 81 | Mut_79 91 0 100 5 91 20 98 0 82 | Mut_80 105 0 93 7 71 16 81 0 83 | Mut_81 108 0 100 13 75 17 88 0 84 | Mut_82 120 0 92 9 82 28 88 0 85 | Mut_83 81 0 120 10 75 19 88 0 86 | Mut_84 77 0 90 11 94 0 86 8 87 | Mut_85 102 0 103 2 105 0 92 5 88 | Mut_86 98 0 100 6 85 0 84 11 89 | Mut_87 101 0 92 7 82 0 104 11 90 | Mut_88 108 0 93 3 95 0 99 4 91 | Mut_89 110 0 108 5 106 0 93 4 92 | Mut_90 96 0 81 6 105 0 94 6 93 | Mut_91 112 0 103 10 96 0 75 11 94 | Mut_92 108 0 98 8 103 0 87 5 95 | Mut_93 97 0 99 0 105 8 89 26 96 | Mut_94 126 0 116 0 94 5 57 19 97 | Mut_95 88 0 110 0 105 7 80 24 98 | Mut_96 97 0 104 0 88 7 70 26 99 | Mut_97 96 0 101 0 89 5 81 32 100 | Mut_98 99 0 96 0 88 5 83 19 101 | Mut_99 97 0 91 5 79 23 93 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_5.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 91 1 97 0 89 11 98 0 3 | Mut_1 88 0 94 0 65 29 93 0 4 | Mut_2 92 0 105 0 68 15 86 0 5 | Mut_3 69 22 94 5 90 0 102 0 6 | Mut_4 73 26 78 2 87 0 102 0 7 | Mut_5 70 23 93 2 92 0 102 0 8 | Mut_6 57 23 104 1 96 0 97 0 9 | Mut_7 67 24 95 3 90 0 116 0 10 | Mut_8 63 38 98 4 101 0 87 0 11 | Mut_9 74 31 106 5 96 0 103 0 12 | Mut_10 69 30 91 2 103 0 98 0 13 | Mut_11 69 45 94 2 87 0 102 0 14 | Mut_12 65 32 98 6 101 0 106 0 15 | Mut_13 80 28 91 2 97 0 76 0 16 | Mut_14 55 28 107 2 112 0 91 0 17 | Mut_15 85 30 92 2 108 0 103 0 18 | Mut_16 58 48 71 12 56 40 64 26 19 | Mut_17 59 41 92 18 63 32 71 20 20 | Mut_18 45 59 83 15 69 37 84 23 21 | Mut_19 60 56 77 20 58 35 68 30 22 | Mut_20 106 2 88 0 87 26 124 0 23 | Mut_21 82 0 96 0 72 14 109 0 24 | Mut_22 98 1 109 0 75 20 112 0 25 | Mut_23 88 0 89 0 83 18 100 0 26 | Mut_24 105 3 110 0 77 16 127 0 27 | Mut_25 96 1 108 0 84 15 77 0 28 | Mut_26 104 0 99 0 83 24 128 0 29 | Mut_27 101 0 103 0 75 18 87 0 30 | Mut_28 108 1 91 0 69 15 107 0 31 | Mut_29 100 0 86 0 75 16 97 0 32 | Mut_30 88 0 93 0 88 19 86 0 33 | Mut_31 74 3 104 0 82 20 87 0 34 | Mut_32 88 0 105 0 72 23 101 0 35 | Mut_33 102 0 86 0 94 22 80 0 36 | Mut_34 115 0 89 0 87 20 84 0 37 | Mut_35 116 1 113 0 80 21 93 0 38 | Mut_36 89 0 84 0 83 30 98 0 39 | Mut_37 100 1 83 0 96 13 94 0 40 | Mut_38 98 0 94 0 80 17 100 0 41 | Mut_39 93 1 110 0 88 20 97 0 42 | Mut_40 89 0 86 0 69 20 80 0 43 | Mut_41 108 1 103 0 79 17 98 0 44 | Mut_42 99 0 97 0 74 27 103 0 45 | Mut_43 86 18 100 0 106 0 104 2 46 | Mut_44 71 16 108 0 90 0 116 1 47 | Mut_45 82 18 112 0 107 0 96 1 48 | Mut_46 89 8 120 0 117 0 116 0 49 | Mut_47 80 15 101 0 89 0 94 0 50 | Mut_48 66 11 91 0 96 0 107 0 51 | Mut_49 84 14 108 0 104 0 101 0 52 | Mut_50 78 18 92 0 107 0 100 1 53 | Mut_51 73 15 105 0 103 0 96 2 54 | Mut_52 100 14 94 0 111 0 96 0 55 | Mut_53 88 14 118 0 109 0 99 0 56 | Mut_54 91 13 80 0 96 0 97 0 57 | Mut_55 84 17 95 0 86 0 90 1 58 | Mut_56 109 15 106 0 120 0 92 0 59 | Mut_57 78 14 95 0 98 0 83 0 60 | Mut_58 88 9 74 0 91 0 118 0 61 | Mut_59 87 10 90 0 91 0 97 1 62 | Mut_60 76 15 85 0 120 0 100 0 63 | Mut_61 65 22 96 0 95 0 92 0 64 | Mut_62 85 19 101 0 90 0 95 0 65 | Mut_63 79 15 101 0 98 0 88 1 66 | Mut_64 88 11 82 0 101 0 94 1 67 | Mut_65 49 51 60 22 62 42 77 26 68 | Mut_66 43 44 72 28 49 47 85 26 69 | Mut_67 55 56 77 19 53 33 70 20 70 | Mut_68 51 42 92 26 69 50 69 26 71 | Mut_69 58 49 69 22 57 48 84 31 72 | Mut_70 50 51 87 22 63 37 60 27 73 | Mut_71 108 0 119 3 96 0 79 22 74 | Mut_72 86 0 100 2 99 0 79 17 75 | Mut_73 96 0 96 1 90 0 89 25 76 | Mut_74 76 0 103 2 89 0 85 18 77 | Mut_75 100 0 97 1 116 0 91 25 78 | Mut_76 68 55 91 15 61 21 80 20 79 | Mut_77 44 44 84 15 73 23 60 19 80 | Mut_78 46 56 88 15 73 21 84 21 81 | Mut_79 56 60 89 17 60 29 84 21 82 | Mut_80 49 54 79 12 82 24 77 24 83 | Mut_81 51 40 94 16 66 24 76 16 84 | Mut_82 40 58 78 20 82 13 84 17 85 | Mut_83 45 55 66 9 68 18 73 23 86 | Mut_84 50 48 93 12 73 23 80 16 87 | Mut_85 37 52 94 10 80 22 83 21 88 | Mut_86 52 36 100 17 91 15 85 21 89 | Mut_87 93 19 72 13 95 0 63 24 90 | Mut_88 83 15 77 13 85 0 76 21 91 | Mut_89 88 15 94 21 99 0 80 18 92 | Mut_90 85 20 91 15 103 0 74 23 93 | Mut_91 84 12 88 16 98 0 95 26 94 | Mut_92 86 13 111 19 91 0 89 19 95 | Mut_93 63 11 81 12 102 0 80 15 96 | Mut_94 72 14 102 16 89 0 90 19 97 | Mut_95 105 12 87 9 109 0 65 23 98 | Mut_96 89 16 90 14 96 0 80 26 99 | Mut_97 85 12 78 9 85 0 82 18 100 | Mut_98 73 20 91 10 101 0 73 25 101 | Mut_99 76 20 96 14 89 0 72 21 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_3.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 76 23 88 18 96 9 70 42 3 | Mut_1 73 27 81 18 92 8 73 39 4 | Mut_2 63 29 74 14 79 10 57 39 5 | Mut_3 106 4 117 2 99 0 99 0 6 | Mut_4 107 3 95 0 94 0 111 0 7 | Mut_5 92 1 96 3 97 0 90 0 8 | Mut_6 89 3 96 3 111 0 95 0 9 | Mut_7 86 4 87 2 86 0 92 0 10 | Mut_8 83 24 72 26 83 16 98 6 11 | Mut_9 77 9 72 27 102 19 101 9 12 | Mut_10 89 18 83 25 79 18 95 2 13 | Mut_11 101 10 74 37 83 13 81 6 14 | Mut_12 73 21 69 32 76 10 100 6 15 | Mut_13 81 13 91 29 78 16 94 6 16 | Mut_14 79 17 61 29 76 20 103 3 17 | Mut_15 62 11 73 35 82 18 85 6 18 | Mut_16 78 15 64 24 84 14 108 1 19 | Mut_17 92 13 79 29 96 19 88 4 20 | Mut_18 84 14 78 32 83 17 91 8 21 | Mut_19 80 21 59 34 78 8 88 4 22 | Mut_20 71 15 70 28 66 10 100 6 23 | Mut_21 83 8 76 34 111 13 88 5 24 | Mut_22 96 18 65 29 90 22 97 4 25 | Mut_23 84 17 78 30 73 19 111 11 26 | Mut_24 79 14 57 38 90 9 81 4 27 | Mut_25 89 16 71 26 70 16 96 4 28 | Mut_26 93 13 63 22 96 11 97 7 29 | Mut_27 84 18 64 32 80 19 110 8 30 | Mut_28 94 18 84 30 90 16 91 6 31 | Mut_29 82 16 70 32 95 15 90 5 32 | Mut_30 95 7 72 29 109 20 90 1 33 | Mut_31 109 15 62 13 64 12 95 4 34 | Mut_32 102 12 77 32 87 14 90 5 35 | Mut_33 79 3 86 1 93 0 93 1 36 | Mut_34 90 1 91 3 98 0 88 0 37 | Mut_35 112 2 106 1 96 0 107 1 38 | Mut_36 90 4 96 1 72 0 88 1 39 | Mut_37 102 4 106 2 101 0 102 0 40 | Mut_38 85 2 107 4 96 0 102 0 41 | Mut_39 53 39 50 53 71 26 60 43 42 | Mut_40 57 34 65 42 83 28 51 37 43 | Mut_41 59 40 53 47 69 33 53 38 44 | Mut_42 54 36 64 47 78 29 57 32 45 | Mut_43 49 41 39 45 78 18 68 35 46 | Mut_44 58 38 47 41 64 23 60 48 47 | Mut_45 50 47 49 50 68 31 60 41 48 | Mut_46 56 50 57 33 72 25 56 39 49 | Mut_47 55 48 45 42 74 22 57 42 50 | Mut_48 78 52 55 39 75 26 63 45 51 | Mut_49 59 55 54 59 74 37 57 44 52 | Mut_50 64 43 49 50 84 39 54 52 53 | Mut_51 71 34 48 50 65 35 59 53 54 | Mut_52 60 50 56 37 70 26 71 35 55 | Mut_53 62 58 41 49 72 22 64 47 56 | Mut_54 62 44 49 36 71 33 62 47 57 | Mut_55 61 43 45 45 57 25 54 33 58 | Mut_56 62 50 45 50 87 24 57 55 59 | Mut_57 44 43 53 54 72 23 54 33 60 | Mut_58 63 49 41 43 74 24 53 41 61 | Mut_59 41 52 45 47 80 31 61 34 62 | Mut_60 58 40 52 41 66 31 40 43 63 | Mut_61 96 5 82 5 112 0 96 0 64 | Mut_62 101 2 115 0 108 0 111 0 65 | Mut_63 99 3 95 3 110 0 85 1 66 | Mut_64 122 5 94 2 107 0 92 0 67 | Mut_65 109 3 103 2 97 0 101 2 68 | Mut_66 97 6 120 4 105 0 100 0 69 | Mut_67 105 6 105 1 102 0 92 0 70 | Mut_68 91 2 92 7 111 0 98 0 71 | Mut_69 105 3 105 4 98 0 91 0 72 | Mut_70 77 7 89 1 84 0 105 0 73 | Mut_71 96 5 92 3 99 0 100 1 74 | Mut_72 97 0 111 4 100 0 98 0 75 | Mut_73 92 1 89 1 122 0 103 0 76 | Mut_74 103 3 92 5 113 0 94 0 77 | Mut_75 115 6 91 4 89 0 94 0 78 | Mut_76 73 31 106 0 94 9 108 0 79 | Mut_77 81 3 85 0 93 21 107 7 80 | Mut_78 110 2 89 0 84 17 86 5 81 | Mut_79 100 1 99 0 72 16 94 1 82 | Mut_80 98 1 91 0 83 17 89 9 83 | Mut_81 95 1 103 0 89 15 103 10 84 | Mut_82 106 1 110 0 83 17 99 7 85 | Mut_83 103 0 83 0 74 11 86 4 86 | Mut_84 81 0 100 0 78 12 111 3 87 | Mut_85 94 2 92 0 92 19 98 9 88 | Mut_86 106 3 109 0 95 13 107 4 89 | Mut_87 80 0 111 0 86 13 89 8 90 | Mut_88 126 2 82 0 96 13 89 6 91 | Mut_89 90 1 128 0 98 3 100 3 92 | Mut_90 102 1 109 0 98 19 97 8 93 | Mut_91 92 6 99 1 86 0 97 0 94 | Mut_92 96 2 103 3 105 0 106 0 95 | Mut_93 98 3 93 4 115 0 106 0 96 | Mut_94 102 0 96 1 109 0 97 0 97 | Mut_95 99 0 99 3 100 0 102 0 98 | Mut_96 124 7 99 4 108 0 100 0 99 | Mut_97 95 4 105 0 101 0 92 0 100 | Mut_98 100 4 102 2 103 0 96 0 101 | Mut_99 126 2 103 1 88 0 95 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_4.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 66 26 93 1 88 22 102 0 3 | Mut_1 83 29 89 1 93 19 99 0 4 | Mut_2 86 22 100 2 82 22 96 0 5 | Mut_3 75 32 97 2 67 12 103 0 6 | Mut_4 70 22 125 1 90 19 113 0 7 | Mut_5 84 32 93 2 106 18 100 0 8 | Mut_6 85 30 99 0 90 15 94 0 9 | Mut_7 76 32 105 1 107 19 108 0 10 | Mut_8 65 29 101 0 83 16 87 0 11 | Mut_9 80 28 105 1 92 15 100 0 12 | Mut_10 84 30 96 1 73 15 92 0 13 | Mut_11 96 13 85 3 104 0 98 0 14 | Mut_12 111 0 99 0 106 0 97 8 15 | Mut_13 105 2 54 44 92 0 78 10 16 | Mut_14 82 2 55 48 93 3 82 11 17 | Mut_15 74 3 59 45 105 4 92 10 18 | Mut_16 89 1 57 40 84 1 84 9 19 | Mut_17 92 7 49 45 96 5 75 10 20 | Mut_18 92 1 46 50 91 1 85 13 21 | Mut_19 100 6 58 44 86 5 94 8 22 | Mut_20 96 4 56 41 83 6 79 9 23 | Mut_21 99 2 62 50 99 3 93 7 24 | Mut_22 104 2 54 48 105 7 74 7 25 | Mut_23 88 2 58 38 101 3 82 9 26 | Mut_24 109 6 54 48 95 3 92 12 27 | Mut_25 89 1 58 42 92 1 82 10 28 | Mut_26 106 3 42 33 98 4 86 10 29 | Mut_27 100 5 58 55 98 1 107 7 30 | Mut_28 97 2 60 45 104 4 111 13 31 | Mut_29 94 5 56 52 96 2 83 9 32 | Mut_30 93 6 57 39 93 4 110 7 33 | Mut_31 105 3 58 55 99 2 96 10 34 | Mut_32 116 3 62 47 102 5 90 11 35 | Mut_33 104 4 58 42 92 2 102 9 36 | Mut_34 96 2 58 51 90 8 92 9 37 | Mut_35 100 9 57 38 94 2 111 0 38 | Mut_36 90 5 56 55 104 1 95 0 39 | Mut_37 83 3 51 43 84 3 88 0 40 | Mut_38 92 1 56 46 92 6 80 0 41 | Mut_39 82 3 53 41 115 4 104 0 42 | Mut_40 106 3 57 51 102 3 103 0 43 | Mut_41 87 1 45 45 85 6 99 0 44 | Mut_42 92 2 53 39 95 3 97 0 45 | Mut_43 100 5 50 39 80 1 93 0 46 | Mut_44 92 2 57 52 98 1 108 0 47 | Mut_45 89 2 45 35 89 2 98 0 48 | Mut_46 80 5 58 54 91 4 89 0 49 | Mut_47 75 2 46 34 87 3 102 0 50 | Mut_48 109 2 43 51 103 1 101 0 51 | Mut_49 97 1 44 46 100 2 95 0 52 | Mut_50 110 4 41 52 110 2 107 0 53 | Mut_51 86 1 56 48 101 6 95 0 54 | Mut_52 94 4 57 46 112 3 87 0 55 | Mut_53 107 2 51 47 89 1 83 0 56 | Mut_54 106 3 55 56 105 2 99 0 57 | Mut_55 108 5 49 50 93 6 98 0 58 | Mut_56 91 5 60 37 95 3 99 0 59 | Mut_57 86 4 66 41 100 2 107 0 60 | Mut_58 82 3 63 39 98 1 109 0 61 | Mut_59 89 1 62 34 114 1 99 0 62 | Mut_60 111 1 68 36 97 4 100 0 63 | Mut_61 111 3 53 58 95 4 83 0 64 | Mut_62 101 4 55 47 89 3 121 0 65 | Mut_63 98 9 64 38 110 2 97 0 66 | Mut_64 107 7 51 40 106 4 88 0 67 | Mut_65 76 0 55 40 112 2 114 0 68 | Mut_66 85 1 60 35 109 5 91 0 69 | Mut_67 112 1 45 48 92 3 107 0 70 | Mut_68 98 2 63 47 105 1 104 0 71 | Mut_69 96 5 50 35 100 2 108 0 72 | Mut_70 80 2 49 45 108 4 95 0 73 | Mut_71 45 56 43 45 59 37 71 24 74 | Mut_72 63 52 56 43 72 24 61 39 75 | Mut_73 48 44 59 77 66 31 74 34 76 | Mut_74 43 54 54 48 77 39 77 38 77 | Mut_75 42 53 46 42 58 40 78 32 78 | Mut_76 38 46 46 32 62 31 56 36 79 | Mut_77 49 66 47 48 56 35 65 24 80 | Mut_78 49 55 47 44 76 28 64 50 81 | Mut_79 48 47 70 51 61 48 57 35 82 | Mut_80 52 34 56 44 57 25 64 32 83 | Mut_81 47 55 51 53 76 34 78 27 84 | Mut_82 60 48 47 66 64 32 63 39 85 | Mut_83 57 43 39 52 53 24 63 21 86 | Mut_84 44 59 53 60 51 34 54 41 87 | Mut_85 52 36 53 57 76 24 59 35 88 | Mut_86 47 47 47 41 64 32 84 43 89 | Mut_87 64 44 42 40 63 37 74 28 90 | Mut_88 53 46 49 45 66 22 60 31 91 | Mut_89 46 49 43 54 75 30 64 24 92 | Mut_90 50 35 100 6 88 14 117 0 93 | Mut_91 57 43 105 5 69 15 106 0 94 | Mut_92 49 43 92 5 85 15 107 0 95 | Mut_93 92 0 101 0 107 7 78 26 96 | Mut_94 103 0 110 0 100 9 61 18 97 | Mut_95 102 0 94 0 74 11 75 32 98 | Mut_96 94 0 101 2 68 21 116 0 99 | Mut_97 60 21 106 2 76 23 106 0 100 | Mut_98 65 32 93 2 65 21 93 0 101 | Mut_99 69 40 111 1 91 24 106 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_2.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 70 26 84 11 101 0 101 0 3 | Mut_1 97 21 87 15 109 0 110 0 4 | Mut_2 93 23 83 19 104 0 107 0 5 | Mut_3 70 21 88 11 102 0 100 0 6 | Mut_4 73 18 86 16 92 0 90 0 7 | Mut_5 79 24 92 19 96 0 86 0 8 | Mut_6 66 20 91 6 96 0 107 0 9 | Mut_7 87 21 63 27 103 0 93 0 10 | Mut_8 83 24 80 15 88 0 95 0 11 | Mut_9 78 31 89 16 115 0 101 0 12 | Mut_10 73 21 69 17 87 0 101 0 13 | Mut_11 78 15 87 15 88 0 104 0 14 | Mut_12 62 38 80 17 110 0 90 0 15 | Mut_13 74 18 92 15 99 0 92 0 16 | Mut_14 80 23 89 12 88 0 90 0 17 | Mut_15 71 24 103 17 83 0 115 0 18 | Mut_16 89 24 70 17 93 0 102 0 19 | Mut_17 78 23 86 23 95 0 106 0 20 | Mut_18 85 29 74 13 97 0 81 0 21 | Mut_19 74 22 92 14 99 0 93 0 22 | Mut_20 84 29 81 18 92 0 95 0 23 | Mut_21 86 21 88 16 85 0 91 0 24 | Mut_22 61 22 85 19 87 0 90 0 25 | Mut_23 86 24 81 16 111 0 99 0 26 | Mut_24 68 19 72 21 92 0 87 0 27 | Mut_25 74 29 79 17 108 0 98 0 28 | Mut_26 74 28 85 20 113 0 106 0 29 | Mut_27 94 0 98 0 101 0 101 0 30 | Mut_28 100 0 103 0 100 0 99 4 31 | Mut_29 94 0 102 0 116 0 98 2 32 | Mut_30 83 15 109 0 58 34 106 0 33 | Mut_31 56 24 109 0 51 49 90 0 34 | Mut_32 77 22 104 0 80 30 98 0 35 | Mut_33 67 19 98 0 73 37 109 0 36 | Mut_34 85 26 101 0 57 45 107 0 37 | Mut_35 61 53 57 53 69 35 42 48 38 | Mut_36 44 45 53 42 62 41 49 67 39 | Mut_37 54 45 44 47 50 52 32 35 40 | Mut_38 62 49 46 43 50 38 37 48 41 | Mut_39 56 48 49 29 59 26 47 49 42 | Mut_40 61 37 44 48 58 48 48 46 43 | Mut_41 58 50 51 41 73 28 49 61 44 | Mut_42 46 59 56 61 54 45 52 46 45 | Mut_43 54 53 53 47 78 39 48 44 46 | Mut_44 51 52 61 50 68 29 48 60 47 | Mut_45 58 35 59 46 59 34 68 39 48 | Mut_46 50 52 54 53 51 46 56 39 49 | Mut_47 53 52 37 35 56 38 47 53 50 | Mut_48 62 50 48 44 69 50 61 36 51 | Mut_49 59 51 51 35 50 51 64 66 52 | Mut_50 54 44 49 60 54 42 60 47 53 | Mut_51 49 43 41 47 58 45 54 54 54 | Mut_52 51 70 59 49 63 37 56 38 55 | Mut_53 36 40 55 41 59 42 60 45 56 | Mut_54 58 58 54 50 57 36 51 56 57 | Mut_55 58 56 52 41 61 28 64 50 58 | Mut_56 74 24 99 0 61 43 95 0 59 | Mut_57 101 0 87 3 80 0 64 33 60 | Mut_58 110 0 71 21 108 2 89 0 61 | Mut_59 107 0 62 29 97 2 103 0 62 | Mut_60 86 0 80 15 94 5 96 0 63 | Mut_61 112 0 80 22 110 5 110 0 64 | Mut_62 85 0 81 26 98 2 108 0 65 | Mut_63 100 0 74 22 99 3 104 0 66 | Mut_64 97 0 63 16 84 5 92 0 67 | Mut_65 101 0 72 28 91 4 101 0 68 | Mut_66 97 0 74 22 108 4 88 0 69 | Mut_67 99 0 89 22 98 2 102 0 70 | Mut_68 111 0 68 18 87 3 93 0 71 | Mut_69 114 0 100 21 92 2 87 0 72 | Mut_70 104 0 74 18 96 6 88 0 73 | Mut_71 107 0 79 27 115 2 99 0 74 | Mut_72 107 0 84 26 93 2 103 0 75 | Mut_73 99 0 87 28 82 1 81 0 76 | Mut_74 96 0 85 27 95 2 84 0 77 | Mut_75 76 0 80 19 88 2 95 0 78 | Mut_76 86 0 81 28 113 3 110 0 79 | Mut_77 104 0 83 18 101 1 93 0 80 | Mut_78 82 0 81 29 109 4 115 0 81 | Mut_79 101 0 88 17 79 2 107 0 82 | Mut_80 84 0 70 23 105 3 105 0 83 | Mut_81 99 0 80 27 93 3 115 0 84 | Mut_82 80 0 78 15 92 2 102 0 85 | Mut_83 117 0 69 27 94 1 97 0 86 | Mut_84 101 0 86 19 97 3 98 0 87 | Mut_85 107 0 71 28 117 1 102 0 88 | Mut_86 115 0 71 25 95 2 92 0 89 | Mut_87 82 0 65 29 93 5 102 0 90 | Mut_88 92 0 59 16 112 4 96 0 91 | Mut_89 78 0 79 25 107 8 107 0 92 | Mut_90 99 0 70 25 86 1 116 0 93 | Mut_91 92 0 76 32 86 5 98 0 94 | Mut_92 113 0 109 2 93 0 84 20 95 | Mut_93 97 0 85 4 85 0 77 14 96 | Mut_94 91 0 98 3 117 0 88 12 97 | Mut_95 101 0 79 3 115 0 88 11 98 | Mut_96 83 0 81 2 101 0 85 12 99 | Mut_97 95 0 100 4 98 0 88 16 100 | Mut_98 77 26 96 4 82 28 75 24 101 | Mut_99 59 26 86 1 61 31 74 30 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_1.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 86 22 77 11 56 33 45 42 3 | Mut_1 55 33 99 11 57 35 65 44 4 | Mut_2 83 23 108 9 60 41 60 41 5 | Mut_3 53 42 104 10 58 27 56 38 6 | Mut_4 67 32 114 13 63 34 66 49 7 | Mut_5 69 40 77 7 67 42 52 38 8 | Mut_6 66 33 108 9 65 32 51 35 9 | Mut_7 55 33 91 3 60 40 51 48 10 | Mut_8 66 32 98 10 61 34 48 42 11 | Mut_9 74 26 84 15 65 34 65 44 12 | Mut_10 81 25 87 8 57 30 42 39 13 | Mut_11 76 21 97 6 68 39 75 39 14 | Mut_12 64 33 92 10 62 42 58 36 15 | Mut_13 75 41 75 9 71 33 50 33 16 | Mut_14 87 34 110 6 58 28 50 50 17 | Mut_15 78 29 92 10 76 29 61 48 18 | Mut_16 81 33 112 7 72 33 51 40 19 | Mut_17 71 21 87 9 66 46 68 43 20 | Mut_18 63 31 86 13 81 30 58 41 21 | Mut_19 65 27 106 10 63 29 64 42 22 | Mut_20 72 26 78 6 85 22 63 44 23 | Mut_21 84 32 93 11 76 40 68 53 24 | Mut_22 80 33 86 8 51 25 49 55 25 | Mut_23 75 32 100 11 75 34 48 46 26 | Mut_24 82 14 81 10 66 29 63 36 27 | Mut_25 71 28 90 8 64 27 73 50 28 | Mut_26 83 32 103 4 76 43 59 43 29 | Mut_27 82 34 101 12 67 40 63 36 30 | Mut_28 70 19 101 7 76 39 47 49 31 | Mut_29 79 33 97 9 66 35 73 40 32 | Mut_30 98 22 84 6 69 28 61 30 33 | Mut_31 77 23 101 7 63 38 49 35 34 | Mut_32 59 21 115 1 110 0 49 44 35 | Mut_33 66 29 95 3 91 0 49 45 36 | Mut_34 75 29 93 2 95 0 56 49 37 | Mut_35 60 33 71 4 96 0 59 45 38 | Mut_36 69 22 98 2 103 0 58 49 39 | Mut_37 65 24 91 2 102 0 57 42 40 | Mut_38 53 26 102 4 106 0 68 41 41 | Mut_39 69 26 81 1 97 0 66 40 42 | Mut_40 75 24 101 2 108 0 61 40 43 | Mut_41 74 36 96 0 111 0 62 44 44 | Mut_42 59 32 75 2 116 0 69 40 45 | Mut_43 78 23 99 0 90 14 93 0 46 | Mut_44 93 25 99 0 106 15 96 0 47 | Mut_45 67 11 94 0 78 10 85 0 48 | Mut_46 63 27 105 0 80 9 90 0 49 | Mut_47 86 17 105 0 85 13 75 0 50 | Mut_48 88 24 97 0 70 20 101 0 51 | Mut_49 75 19 110 0 81 14 103 0 52 | Mut_50 99 20 111 0 83 19 97 0 53 | Mut_51 53 44 51 38 35 44 51 42 54 | Mut_52 83 26 102 4 106 0 96 0 55 | Mut_53 84 0 105 0 80 12 97 0 56 | Mut_54 82 7 89 0 110 0 65 49 57 | Mut_55 96 5 90 0 108 0 52 43 58 | Mut_56 94 7 85 0 106 0 65 44 59 | Mut_57 99 2 110 0 96 0 57 43 60 | Mut_58 95 5 116 0 96 0 53 48 61 | Mut_59 101 4 103 0 118 0 54 45 62 | Mut_60 86 8 108 0 88 0 57 51 63 | Mut_61 81 6 80 0 98 0 62 57 64 | Mut_62 111 10 117 0 86 0 66 39 65 | Mut_63 97 4 108 0 87 0 58 39 66 | Mut_64 70 0 73 35 98 0 96 0 67 | Mut_65 95 0 74 32 92 0 104 0 68 | Mut_66 99 0 77 32 93 0 97 0 69 | Mut_67 103 0 102 2 86 8 92 0 70 | Mut_68 93 0 100 0 77 15 93 0 71 | Mut_69 107 0 102 0 95 18 92 0 72 | Mut_70 105 0 121 0 83 14 98 0 73 | Mut_71 102 0 94 2 76 13 97 0 74 | Mut_72 115 0 107 2 92 15 92 0 75 | Mut_73 103 0 111 1 81 16 97 0 76 | Mut_74 102 0 99 1 89 11 91 0 77 | Mut_75 103 0 105 0 86 11 106 0 78 | Mut_76 130 0 110 0 85 10 111 0 79 | Mut_77 102 0 114 2 76 20 104 0 80 | Mut_78 104 0 117 0 77 14 116 0 81 | Mut_79 108 0 96 0 80 20 90 0 82 | Mut_80 99 0 80 1 80 16 106 0 83 | Mut_81 113 0 87 0 83 14 111 0 84 | Mut_82 102 0 85 2 73 14 111 0 85 | Mut_83 100 0 103 2 83 9 119 0 86 | Mut_84 102 0 104 1 69 12 104 0 87 | Mut_85 96 0 92 3 91 16 89 0 88 | Mut_86 96 0 90 0 96 14 100 0 89 | Mut_87 89 0 95 2 100 11 91 0 90 | Mut_88 92 0 115 0 99 10 97 0 91 | Mut_89 92 0 103 2 89 9 94 0 92 | Mut_90 93 0 120 0 80 14 107 0 93 | Mut_91 103 0 107 1 84 18 79 0 94 | Mut_92 105 0 93 1 79 18 91 0 95 | Mut_93 106 0 92 3 71 17 102 0 96 | Mut_94 95 0 96 6 80 7 128 0 97 | Mut_95 95 0 98 4 80 14 103 0 98 | Mut_96 77 0 99 3 70 22 107 0 99 | Mut_97 85 0 92 4 87 16 87 0 100 | Mut_98 100 0 97 8 81 10 94 0 101 | Mut_99 104 0 88 1 78 8 86 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_8.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 85 14 98 0 116 0 116 0 3 | Mut_1 88 8 94 0 95 0 109 0 4 | Mut_2 105 10 107 0 90 0 107 0 5 | Mut_3 82 6 104 0 98 0 94 1 6 | Mut_4 89 8 96 0 101 0 100 0 7 | Mut_5 90 9 111 0 98 0 112 0 8 | Mut_6 85 10 112 0 103 0 119 0 9 | Mut_7 80 6 103 0 95 0 89 1 10 | Mut_8 95 7 104 0 109 0 96 0 11 | Mut_9 93 6 84 0 107 0 104 0 12 | Mut_10 99 12 102 0 89 0 95 0 13 | Mut_11 94 10 109 0 89 0 103 0 14 | Mut_12 96 12 94 0 104 0 101 0 15 | Mut_13 79 12 96 0 94 0 111 0 16 | Mut_14 116 5 106 0 102 0 93 0 17 | Mut_15 89 15 94 0 93 19 97 0 18 | Mut_16 87 11 119 0 90 16 108 0 19 | Mut_17 78 13 103 0 79 24 114 0 20 | Mut_18 104 0 84 0 86 1 108 16 21 | Mut_19 88 0 99 0 109 5 78 12 22 | Mut_20 90 0 84 0 86 1 94 8 23 | Mut_21 115 0 110 0 99 1 93 15 24 | Mut_22 82 0 94 0 108 2 92 19 25 | Mut_23 122 0 89 0 117 2 98 10 26 | Mut_24 94 0 108 0 91 2 68 12 27 | Mut_25 94 0 91 0 99 4 111 6 28 | Mut_26 95 0 111 0 91 4 89 16 29 | Mut_27 98 0 100 0 101 3 94 17 30 | Mut_28 97 0 105 0 110 1 106 14 31 | Mut_29 92 0 110 0 106 1 78 11 32 | Mut_30 112 0 107 0 78 0 79 17 33 | Mut_31 65 40 48 39 58 37 59 37 34 | Mut_32 52 24 64 38 53 30 65 47 35 | Mut_33 49 37 67 37 60 44 62 46 36 | Mut_34 51 44 54 38 54 35 57 40 37 | Mut_35 57 37 55 40 52 42 50 33 38 | Mut_36 65 48 62 25 53 52 65 52 39 | Mut_37 55 46 61 27 60 40 58 44 40 | Mut_38 48 41 60 34 52 31 74 37 41 | Mut_39 49 27 66 48 54 45 81 44 42 | Mut_40 61 41 76 43 64 38 60 39 43 | Mut_41 59 45 65 31 66 44 64 42 44 | Mut_42 86 8 96 0 89 0 106 0 45 | Mut_43 104 9 96 0 106 0 102 0 46 | Mut_44 100 12 104 0 96 0 108 0 47 | Mut_45 111 8 108 0 98 0 101 0 48 | Mut_46 98 9 96 0 103 0 104 0 49 | Mut_47 77 12 104 0 102 0 122 0 50 | Mut_48 97 0 87 14 120 0 88 27 51 | Mut_49 96 0 89 15 122 0 77 19 52 | Mut_50 89 0 85 19 100 0 76 27 53 | Mut_51 111 0 72 19 97 0 73 27 54 | Mut_52 109 0 87 19 91 0 71 24 55 | Mut_53 100 0 89 14 102 0 60 21 56 | Mut_54 101 0 75 12 95 0 65 32 57 | Mut_55 110 0 76 26 94 0 75 27 58 | Mut_56 101 0 82 17 101 0 69 25 59 | Mut_57 91 10 91 16 73 0 86 1 60 | Mut_58 86 4 81 17 103 0 101 0 61 | Mut_59 93 9 68 16 105 0 103 3 62 | Mut_60 83 9 77 14 104 0 90 2 63 | Mut_61 98 11 84 19 93 0 109 0 64 | Mut_62 98 9 85 14 95 0 91 1 65 | Mut_63 100 10 82 16 99 0 99 2 66 | Mut_64 78 9 98 17 110 0 87 1 67 | Mut_65 89 11 77 18 105 0 98 0 68 | Mut_66 88 14 70 21 96 2 80 22 69 | Mut_67 70 23 88 16 94 4 90 16 70 | Mut_68 72 14 76 21 128 1 96 14 71 | Mut_69 73 17 99 15 110 0 97 15 72 | Mut_70 102 18 85 7 94 1 104 18 73 | Mut_71 85 14 68 14 87 3 80 18 74 | Mut_72 86 25 88 19 93 2 87 12 75 | Mut_73 78 17 82 14 82 1 83 11 76 | Mut_74 77 18 84 14 93 2 83 7 77 | Mut_75 63 15 82 18 88 3 92 16 78 | Mut_76 72 19 84 21 102 2 92 19 79 | Mut_77 87 23 93 15 108 2 80 15 80 | Mut_78 72 19 71 15 86 2 82 14 81 | Mut_79 65 22 83 17 105 1 81 10 82 | Mut_80 89 15 85 20 103 4 65 6 83 | Mut_81 84 17 94 18 100 1 91 13 84 | Mut_82 73 24 75 13 98 0 79 10 85 | Mut_83 88 24 103 12 98 3 93 11 86 | Mut_84 106 26 72 23 106 1 83 9 87 | Mut_85 78 14 76 17 101 2 75 12 88 | Mut_86 97 15 90 19 91 5 91 21 89 | Mut_87 81 23 83 17 100 1 81 16 90 | Mut_88 60 28 105 15 95 2 92 17 91 | Mut_89 76 22 95 14 96 3 71 12 92 | Mut_90 93 27 91 18 105 3 79 4 93 | Mut_91 91 4 78 23 110 0 132 0 94 | Mut_92 78 6 73 12 107 0 88 0 95 | Mut_93 82 6 85 15 94 0 88 0 96 | Mut_94 79 4 77 21 99 0 73 0 97 | Mut_95 89 11 64 17 107 0 95 0 98 | Mut_96 108 6 92 16 95 0 101 0 99 | Mut_97 95 4 87 15 97 0 107 0 100 | Mut_98 82 6 71 15 101 0 102 0 101 | Mut_99 98 6 87 13 88 0 89 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_7.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 91 0 86 11 78 26 90 8 3 | Mut_1 109 0 82 21 61 22 81 9 4 | Mut_2 87 2 81 12 62 41 89 16 5 | Mut_3 67 4 89 12 88 40 91 9 6 | Mut_4 92 3 75 19 91 27 78 9 7 | Mut_5 98 5 92 17 82 26 111 9 8 | Mut_6 99 4 88 18 66 25 106 14 9 | Mut_7 82 1 75 17 75 29 77 6 10 | Mut_8 109 3 77 21 80 34 85 12 11 | Mut_9 87 1 74 16 74 16 94 0 12 | Mut_10 100 0 103 1 92 0 91 12 13 | Mut_11 89 0 102 0 101 0 87 6 14 | Mut_12 112 0 92 0 101 0 72 8 15 | Mut_13 93 0 91 0 108 0 81 6 16 | Mut_14 100 0 106 0 116 0 98 6 17 | Mut_15 104 0 101 0 96 0 85 11 18 | Mut_16 101 0 96 0 93 0 92 12 19 | Mut_17 104 0 109 0 114 0 96 4 20 | Mut_18 106 0 98 0 107 0 86 10 21 | Mut_19 101 0 104 0 103 0 99 6 22 | Mut_20 110 0 96 0 101 0 80 10 23 | Mut_21 99 0 114 0 94 0 94 5 24 | Mut_22 92 0 107 0 113 0 111 12 25 | Mut_23 108 0 82 0 108 0 86 8 26 | Mut_24 97 0 105 0 97 0 83 11 27 | Mut_25 95 0 115 0 102 0 81 7 28 | Mut_26 90 0 92 0 83 0 92 8 29 | Mut_27 114 0 103 0 101 0 69 13 30 | Mut_28 97 0 80 0 88 0 112 14 31 | Mut_29 95 0 90 0 97 0 91 13 32 | Mut_30 108 0 88 0 102 0 92 9 33 | Mut_31 82 0 95 0 107 0 78 6 34 | Mut_32 109 3 103 0 94 19 105 0 35 | Mut_33 100 9 100 0 80 20 107 0 36 | Mut_34 89 5 110 0 75 22 111 0 37 | Mut_35 92 5 104 0 73 15 101 0 38 | Mut_36 103 0 60 16 107 0 90 0 39 | Mut_37 91 0 88 21 99 0 120 0 40 | Mut_38 87 0 77 17 100 0 104 0 41 | Mut_39 111 0 86 25 102 0 106 0 42 | Mut_40 98 0 66 25 97 0 90 0 43 | Mut_41 88 0 85 21 100 0 89 0 44 | Mut_42 88 0 101 29 95 0 108 0 45 | Mut_43 101 6 107 0 86 19 115 0 46 | Mut_44 98 5 98 0 99 20 96 0 47 | Mut_45 100 7 82 0 69 18 96 0 48 | Mut_46 96 10 83 0 91 17 105 0 49 | Mut_47 94 3 118 0 63 20 97 0 50 | Mut_48 92 5 88 0 84 25 87 0 51 | Mut_49 89 6 89 0 91 19 110 0 52 | Mut_50 100 7 114 0 102 17 106 0 53 | Mut_51 88 8 92 0 83 21 104 0 54 | Mut_52 104 2 108 0 92 23 129 0 55 | Mut_53 98 6 89 0 70 17 94 0 56 | Mut_54 91 3 96 0 89 20 113 0 57 | Mut_55 84 11 101 0 77 20 94 0 58 | Mut_56 95 6 98 0 77 15 117 0 59 | Mut_57 85 8 100 0 75 10 88 0 60 | Mut_58 88 5 118 0 66 14 99 0 61 | Mut_59 96 7 98 0 88 23 98 0 62 | Mut_60 52 57 53 39 56 57 63 35 63 | Mut_61 49 52 60 42 54 53 69 29 64 | Mut_62 46 45 58 44 56 66 74 34 65 | Mut_63 61 46 67 36 51 46 67 35 66 | Mut_64 43 43 63 50 51 44 67 43 67 | Mut_65 54 46 69 46 46 54 65 29 68 | Mut_66 32 43 70 33 52 56 76 35 69 | Mut_67 42 45 67 40 53 44 56 34 70 | Mut_68 53 50 52 34 51 44 64 30 71 | Mut_69 53 42 54 50 61 63 73 34 72 | Mut_70 57 49 57 43 59 51 63 33 73 | Mut_71 51 35 53 53 46 43 77 30 74 | Mut_72 56 50 57 53 43 45 67 28 75 | Mut_73 47 48 61 43 55 50 52 29 76 | Mut_74 66 54 67 48 57 47 58 27 77 | Mut_75 58 46 54 45 60 38 61 36 78 | Mut_76 52 36 49 29 49 66 85 32 79 | Mut_77 60 52 55 45 50 43 72 33 80 | Mut_78 43 41 58 39 47 46 67 37 81 | Mut_79 42 69 63 41 66 49 64 26 82 | Mut_80 52 61 60 45 48 42 59 37 83 | Mut_81 56 47 58 43 44 46 71 34 84 | Mut_82 53 37 46 46 55 42 70 34 85 | Mut_83 47 57 59 42 66 53 61 26 86 | Mut_84 49 49 51 47 50 42 71 38 87 | Mut_85 53 55 53 26 47 40 69 41 88 | Mut_86 109 0 76 16 64 34 124 0 89 | Mut_87 105 0 80 9 72 34 98 0 90 | Mut_88 100 0 78 20 75 32 104 0 91 | Mut_89 109 0 84 12 75 29 98 0 92 | Mut_90 98 0 85 15 62 31 81 0 93 | Mut_91 94 0 87 15 48 28 87 0 94 | Mut_92 116 0 82 19 57 28 97 0 95 | Mut_93 105 0 79 11 76 19 103 0 96 | Mut_94 97 0 89 22 78 30 115 0 97 | Mut_95 106 0 83 12 63 35 90 0 98 | Mut_96 67 32 105 9 109 0 93 0 99 | Mut_97 82 16 58 39 60 61 68 14 100 | Mut_98 73 10 56 37 51 47 99 15 101 | Mut_99 85 18 58 41 42 44 72 12 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_0.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 97 0 94 9 109 0 92 0 3 | Mut_1 107 0 88 13 96 1 111 0 4 | Mut_2 86 0 90 19 78 0 86 0 5 | Mut_3 97 0 78 14 82 1 80 0 6 | Mut_4 95 0 80 16 95 1 85 0 7 | Mut_5 104 0 88 18 89 0 113 0 8 | Mut_6 116 0 87 22 82 0 123 0 9 | Mut_7 101 0 84 14 87 1 88 0 10 | Mut_8 96 0 103 18 90 0 103 0 11 | Mut_9 101 0 86 13 96 0 103 0 12 | Mut_10 88 0 81 20 113 0 129 0 13 | Mut_11 84 21 74 26 80 12 86 0 14 | Mut_12 89 17 68 26 78 17 103 0 15 | Mut_13 81 14 75 21 90 12 116 0 16 | Mut_14 68 17 101 31 76 13 105 0 17 | Mut_15 75 18 67 22 97 16 85 0 18 | Mut_16 91 19 64 20 87 21 111 0 19 | Mut_17 87 16 77 25 71 21 99 0 20 | Mut_18 78 23 95 15 73 21 112 0 21 | Mut_19 73 11 83 33 90 15 101 0 22 | Mut_20 88 20 81 22 95 20 96 0 23 | Mut_21 72 19 72 23 78 25 92 0 24 | Mut_22 75 15 74 15 100 0 83 0 25 | Mut_23 93 15 77 16 103 0 98 0 26 | Mut_24 93 17 73 10 109 0 98 0 27 | Mut_25 85 12 79 18 111 0 103 0 28 | Mut_26 79 13 95 26 90 0 85 0 29 | Mut_27 69 18 88 18 107 0 94 0 30 | Mut_28 92 11 89 23 94 0 101 0 31 | Mut_29 104 14 70 10 97 0 105 0 32 | Mut_30 78 12 83 16 119 0 102 0 33 | Mut_31 96 7 87 23 98 0 100 0 34 | Mut_32 71 8 75 20 98 0 118 0 35 | Mut_33 81 11 83 16 96 0 115 0 36 | Mut_34 92 13 83 22 124 0 99 0 37 | Mut_35 70 13 85 24 105 0 109 0 38 | Mut_36 106 13 70 13 99 0 107 0 39 | Mut_37 69 11 100 16 106 0 101 0 40 | Mut_38 99 16 101 20 104 0 103 0 41 | Mut_39 79 14 74 24 102 0 98 0 42 | Mut_40 76 14 81 11 104 0 92 0 43 | Mut_41 81 14 88 20 88 0 110 0 44 | Mut_42 79 10 81 18 93 0 106 0 45 | Mut_43 90 14 87 18 100 0 91 0 46 | Mut_44 84 12 91 15 93 0 108 0 47 | Mut_45 92 13 62 22 94 0 95 0 48 | Mut_46 79 12 84 14 100 0 90 0 49 | Mut_47 77 11 96 17 117 0 103 0 50 | Mut_48 80 17 79 19 115 0 104 0 51 | Mut_49 98 3 89 11 89 0 92 0 52 | Mut_50 104 0 72 16 87 0 116 0 53 | Mut_51 100 4 99 11 112 0 95 0 54 | Mut_52 94 4 71 14 87 0 113 0 55 | Mut_53 103 3 86 11 99 1 105 0 56 | Mut_54 89 0 72 11 109 0 96 0 57 | Mut_55 77 31 114 0 66 32 92 19 58 | Mut_56 72 25 106 0 62 31 80 15 59 | Mut_57 45 55 63 37 49 48 80 16 60 | Mut_58 43 47 70 43 49 51 83 20 61 | Mut_59 51 38 64 43 69 40 82 14 62 | Mut_60 47 49 46 35 56 50 91 23 63 | Mut_61 56 41 62 49 68 45 80 14 64 | Mut_62 62 48 59 44 52 51 76 25 65 | Mut_63 47 54 63 40 48 58 70 18 66 | Mut_64 59 42 70 36 57 41 80 17 67 | Mut_65 58 57 59 41 58 41 81 28 68 | Mut_66 63 53 50 33 65 46 88 26 69 | Mut_67 52 50 62 34 59 40 79 20 70 | Mut_68 50 51 67 38 60 54 90 15 71 | Mut_69 48 48 62 43 36 38 99 17 72 | Mut_70 36 49 70 42 55 37 76 20 73 | Mut_71 52 67 60 34 63 45 79 21 74 | Mut_72 57 37 62 47 45 43 76 24 75 | Mut_73 56 50 60 38 50 36 78 19 76 | Mut_74 53 50 59 47 63 46 74 15 77 | Mut_75 58 51 60 40 57 43 88 15 78 | Mut_76 39 58 73 48 37 42 82 17 79 | Mut_77 65 42 65 31 44 41 76 24 80 | Mut_78 66 41 64 45 64 60 72 19 81 | Mut_79 45 43 57 51 51 55 75 20 82 | Mut_80 56 34 55 41 47 52 99 20 83 | Mut_81 58 55 46 42 58 40 69 22 84 | Mut_82 51 43 70 33 44 51 90 17 85 | Mut_83 58 45 65 41 58 52 61 21 86 | Mut_84 44 46 65 38 50 41 90 11 87 | Mut_85 46 49 59 44 57 58 85 20 88 | Mut_86 50 47 57 39 64 48 77 24 89 | Mut_87 49 47 73 32 42 45 76 18 90 | Mut_88 70 29 115 0 76 15 90 0 91 | Mut_89 77 31 84 0 86 21 120 0 92 | Mut_90 73 24 118 0 86 30 101 0 93 | Mut_91 95 4 106 1 105 5 103 0 94 | Mut_92 95 3 106 1 90 8 98 0 95 | Mut_93 115 4 86 0 80 10 105 0 96 | Mut_94 91 3 101 1 106 5 113 0 97 | Mut_95 100 4 92 1 96 8 98 0 98 | Mut_96 110 0 89 1 84 9 100 0 99 | Mut_97 91 0 106 4 87 9 89 0 100 | Mut_98 104 0 92 4 88 14 115 0 101 | Mut_99 107 0 98 6 82 14 102 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_4_Mut_100_Clone_10_PCR_Removed/sim_9.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 2 | Mut_0 63 23 81 21 74 28 88 3 3 | Mut_1 89 23 87 10 83 22 108 10 4 | Mut_2 91 17 84 10 78 10 80 9 5 | Mut_3 77 15 98 18 86 17 99 5 6 | Mut_4 94 19 76 15 84 19 94 5 7 | Mut_5 85 20 66 10 82 23 80 11 8 | Mut_6 86 16 78 16 92 11 101 7 9 | Mut_7 92 24 77 9 84 21 96 6 10 | Mut_8 77 27 88 10 89 29 86 6 11 | Mut_9 76 21 73 19 93 20 99 5 12 | Mut_10 82 23 83 13 79 10 102 7 13 | Mut_11 58 25 79 14 84 0 78 0 14 | Mut_12 75 23 106 14 118 0 81 0 15 | Mut_13 90 19 88 15 90 0 109 0 16 | Mut_14 82 19 87 13 105 0 90 0 17 | Mut_15 81 15 105 6 116 0 99 0 18 | Mut_16 90 24 76 15 104 0 100 0 19 | Mut_17 80 19 91 16 104 0 95 0 20 | Mut_18 76 29 101 12 107 0 104 0 21 | Mut_19 90 25 75 13 107 0 100 0 22 | Mut_20 76 18 85 20 82 15 79 7 23 | Mut_21 90 22 84 17 74 25 95 5 24 | Mut_22 75 24 92 11 77 18 98 2 25 | Mut_23 74 24 84 14 83 16 78 9 26 | Mut_24 83 29 91 14 90 27 90 7 27 | Mut_25 70 21 86 20 78 17 88 7 28 | Mut_26 69 17 77 14 85 23 102 6 29 | Mut_27 67 25 85 17 77 28 92 12 30 | Mut_28 62 25 74 11 90 23 104 5 31 | Mut_29 90 23 77 19 79 13 103 4 32 | Mut_30 84 18 79 22 83 19 94 6 33 | Mut_31 93 24 99 9 100 14 99 7 34 | Mut_32 78 18 101 12 81 18 114 5 35 | Mut_33 67 24 72 9 80 18 96 10 36 | Mut_34 105 25 97 11 78 27 99 11 37 | Mut_35 65 20 90 13 96 25 90 6 38 | Mut_36 80 34 84 11 84 17 89 8 39 | Mut_37 78 17 102 10 91 21 95 7 40 | Mut_38 82 22 68 16 81 13 102 8 41 | Mut_39 81 17 95 14 75 16 69 9 42 | Mut_40 67 17 84 16 78 24 107 3 43 | Mut_41 77 18 99 14 76 21 95 4 44 | Mut_42 80 17 83 20 95 14 76 10 45 | Mut_43 71 26 87 16 65 27 87 6 46 | Mut_44 74 32 72 12 85 18 87 5 47 | Mut_45 91 29 69 11 82 15 81 4 48 | Mut_46 93 20 77 19 94 19 88 7 49 | Mut_47 115 0 103 0 98 13 76 5 50 | Mut_48 92 0 106 0 99 9 94 7 51 | Mut_49 80 0 88 0 78 21 86 10 52 | Mut_50 94 0 91 0 88 27 65 6 53 | Mut_51 84 0 87 0 63 17 94 10 54 | Mut_52 96 0 99 0 71 26 107 11 55 | Mut_53 75 0 111 0 82 15 98 6 56 | Mut_54 95 0 100 0 84 21 87 8 57 | Mut_55 113 0 122 0 84 20 83 8 58 | Mut_56 110 0 96 0 77 16 94 8 59 | Mut_57 99 0 92 0 78 20 82 5 60 | Mut_58 101 0 100 0 78 21 115 9 61 | Mut_59 104 0 80 0 84 22 100 10 62 | Mut_60 112 0 108 0 88 21 97 7 63 | Mut_61 98 0 90 0 95 18 86 6 64 | Mut_62 87 0 97 0 91 14 104 4 65 | Mut_63 71 0 95 8 78 16 77 1 66 | Mut_64 74 18 74 11 108 0 99 0 67 | Mut_65 72 18 99 12 103 0 90 0 68 | Mut_66 89 25 83 15 116 0 100 0 69 | Mut_67 92 26 100 20 118 0 95 0 70 | Mut_68 59 43 58 45 59 34 65 49 71 | Mut_69 68 41 48 30 61 42 45 45 72 | Mut_70 76 35 47 41 48 37 45 51 73 | Mut_71 59 44 61 43 59 46 51 45 74 | Mut_72 69 57 79 45 61 31 55 57 75 | Mut_73 64 34 54 50 65 29 52 57 76 | Mut_74 70 31 62 33 62 38 50 50 77 | Mut_75 61 41 58 39 61 35 39 46 78 | Mut_76 65 38 55 50 67 45 54 45 79 | Mut_77 65 49 59 32 61 45 52 50 80 | Mut_78 66 41 61 31 67 35 48 56 81 | Mut_79 64 41 59 47 60 37 45 49 82 | Mut_80 76 37 75 41 77 44 57 55 83 | Mut_81 61 44 77 42 62 43 40 41 84 | Mut_82 66 40 46 34 77 41 47 51 85 | Mut_83 74 33 54 33 70 35 32 48 86 | Mut_84 75 33 51 52 61 35 58 61 87 | Mut_85 59 40 58 34 65 36 72 54 88 | Mut_86 98 11 71 19 109 0 111 0 89 | Mut_87 98 11 58 22 113 0 110 0 90 | Mut_88 87 9 85 21 122 0 95 0 91 | Mut_89 89 11 85 17 82 0 81 0 92 | Mut_90 72 9 68 26 114 0 109 0 93 | Mut_91 79 10 80 24 108 0 87 0 94 | Mut_92 88 12 86 19 96 0 89 0 95 | Mut_93 88 8 73 14 91 0 97 0 96 | Mut_94 73 17 83 20 93 0 106 0 97 | Mut_95 95 9 74 14 98 0 113 0 98 | Mut_96 96 6 84 15 96 0 105 0 99 | Mut_97 67 23 75 10 88 20 86 15 100 | Mut_98 55 35 54 41 78 24 52 47 101 | Mut_99 65 30 69 57 78 30 52 42 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_6.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 58 0 56 1 37 22 48 10 22 22 3 | Mut_1 58 0 47 3 40 9 38 10 27 24 4 | Mut_2 39 0 43 2 29 12 36 9 36 24 5 | Mut_3 56 0 38 2 56 16 47 8 28 17 6 | Mut_4 45 0 36 0 34 14 26 9 19 36 7 | Mut_5 52 0 40 0 39 16 46 13 27 22 8 | Mut_6 55 0 40 1 45 0 48 0 49 0 9 | Mut_7 49 1 47 1 53 0 48 0 34 0 10 | Mut_8 44 0 58 0 48 0 56 0 51 0 11 | Mut_9 54 1 57 0 50 0 37 0 30 0 12 | Mut_10 49 0 52 0 63 0 45 0 43 0 13 | Mut_11 61 0 50 0 45 0 58 0 44 0 14 | Mut_12 55 0 52 1 53 0 47 0 45 0 15 | Mut_13 38 0 54 1 43 0 45 0 50 0 16 | Mut_14 48 0 45 0 55 0 59 0 60 0 17 | Mut_15 51 0 54 1 54 0 55 0 53 0 18 | Mut_16 45 0 47 0 63 0 49 0 43 0 19 | Mut_17 66 0 45 0 51 0 40 0 42 0 20 | Mut_18 55 0 51 2 68 0 49 0 53 0 21 | Mut_19 49 0 42 2 42 0 50 0 52 0 22 | Mut_20 52 0 59 1 48 0 51 0 53 0 23 | Mut_21 63 0 53 0 40 0 53 0 44 0 24 | Mut_22 50 0 59 1 47 0 43 0 46 0 25 | Mut_23 48 0 22 16 48 0 40 2 52 1 26 | Mut_24 54 0 24 19 40 0 47 2 49 0 27 | Mut_25 47 0 31 21 48 0 46 8 63 0 28 | Mut_26 58 0 33 20 48 0 48 3 55 0 29 | Mut_27 53 0 30 21 52 0 42 5 43 0 30 | Mut_28 45 0 34 16 39 0 48 7 58 0 31 | Mut_29 53 0 60 0 49 0 42 12 58 3 32 | Mut_30 43 0 51 0 58 0 37 5 55 2 33 | Mut_31 48 0 53 0 43 0 35 11 47 2 34 | Mut_32 56 0 41 0 44 0 36 14 45 1 35 | Mut_33 49 0 44 0 39 0 28 6 43 3 36 | Mut_34 56 0 51 0 59 0 41 14 57 0 37 | Mut_35 48 0 45 0 52 0 46 10 42 2 38 | Mut_36 53 0 44 0 55 0 35 7 61 2 39 | Mut_37 47 0 43 0 49 0 55 13 61 2 40 | Mut_38 49 0 43 0 45 0 28 12 50 2 41 | Mut_39 55 0 51 0 46 0 39 5 60 1 42 | Mut_40 48 0 48 0 54 0 28 12 37 4 43 | Mut_41 43 0 53 0 53 0 38 4 47 1 44 | Mut_42 52 0 60 0 48 0 50 11 59 1 45 | Mut_43 51 0 52 0 60 0 51 4 58 3 46 | Mut_44 52 0 37 0 57 0 44 13 48 4 47 | Mut_45 55 0 49 0 66 0 44 7 53 0 48 | Mut_46 52 0 46 0 49 0 45 8 50 0 49 | Mut_47 44 0 47 0 64 0 46 6 43 3 50 | Mut_48 33 0 52 0 46 0 47 8 42 0 51 | Mut_49 56 0 48 0 47 0 50 2 56 3 52 | Mut_50 49 0 46 0 45 3 55 3 58 0 53 | Mut_51 45 0 41 0 44 4 46 5 54 0 54 | Mut_52 44 0 55 0 37 7 46 1 55 0 55 | Mut_53 59 0 47 0 44 4 44 1 44 0 56 | Mut_54 43 0 48 0 51 9 52 3 58 0 57 | Mut_55 57 0 50 0 43 2 48 2 41 0 58 | Mut_56 52 0 68 0 49 7 61 2 60 0 59 | Mut_57 50 0 37 0 34 3 40 2 49 0 60 | Mut_58 50 0 59 0 62 8 39 0 42 0 61 | Mut_59 57 0 49 0 47 8 59 2 46 0 62 | Mut_60 56 0 64 0 53 7 56 0 44 0 63 | Mut_61 43 0 57 0 28 9 50 3 43 0 64 | Mut_62 46 0 61 0 35 8 44 3 63 0 65 | Mut_63 45 0 56 0 34 7 55 3 48 0 66 | Mut_64 48 0 49 0 44 5 53 3 48 0 67 | Mut_65 55 0 58 0 51 7 40 3 39 0 68 | Mut_66 61 0 57 0 48 3 44 2 41 0 69 | Mut_67 54 0 43 0 42 3 44 0 46 0 70 | Mut_68 53 0 40 0 44 7 43 1 43 0 71 | Mut_69 45 0 59 0 56 4 47 6 39 0 72 | Mut_70 52 0 54 0 40 9 42 1 38 0 73 | Mut_71 43 0 46 0 43 6 48 6 43 0 74 | Mut_72 54 0 57 0 48 10 42 6 49 0 75 | Mut_73 58 0 47 0 50 7 45 3 45 0 76 | Mut_74 54 0 53 0 48 12 53 0 35 0 77 | Mut_75 52 0 51 0 42 5 58 1 57 0 78 | Mut_76 54 0 53 0 34 4 47 2 64 0 79 | Mut_77 50 0 45 0 41 7 57 4 56 0 80 | Mut_78 42 0 55 0 51 4 58 6 42 0 81 | Mut_79 47 0 51 0 38 8 50 1 52 0 82 | Mut_80 45 0 64 0 46 11 45 4 50 0 83 | Mut_81 58 0 56 0 46 9 41 1 41 0 84 | Mut_82 42 0 44 0 50 4 48 3 51 0 85 | Mut_83 41 0 43 0 48 6 50 0 38 0 86 | Mut_84 46 0 39 0 47 8 48 1 53 0 87 | Mut_85 53 0 54 0 42 6 40 3 66 0 88 | Mut_86 41 0 43 0 47 3 42 3 40 0 89 | Mut_87 36 9 48 0 38 10 42 20 27 24 90 | Mut_88 35 6 31 17 42 15 45 10 29 24 91 | Mut_89 60 0 59 0 43 11 49 0 35 20 92 | Mut_90 40 14 33 19 25 10 24 16 30 32 93 | Mut_91 33 19 28 21 33 33 38 16 29 23 94 | Mut_92 40 12 27 17 32 27 21 21 27 26 95 | Mut_93 57 0 52 0 45 0 54 0 45 4 96 | Mut_94 63 0 64 0 48 0 43 0 43 9 97 | Mut_95 50 0 44 2 51 0 67 0 36 8 98 | Mut_96 51 0 67 2 47 0 41 0 39 6 99 | Mut_97 51 0 56 1 60 1 55 0 43 5 100 | Mut_98 49 0 38 1 45 0 54 0 40 5 101 | Mut_99 49 0 55 1 59 0 57 0 46 5 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_9.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 47 0 47 0 42 3 53 5 50 0 3 | Mut_1 35 7 49 4 29 3 43 1 51 0 4 | Mut_2 52 16 31 5 40 8 47 4 40 0 5 | Mut_3 34 10 47 5 39 10 45 4 44 0 6 | Mut_4 34 7 48 3 41 15 36 0 60 0 7 | Mut_5 41 8 36 4 27 7 42 2 48 0 8 | Mut_6 47 9 47 6 31 9 47 2 67 0 9 | Mut_7 33 3 34 11 42 9 34 1 58 0 10 | Mut_8 41 6 42 3 42 8 35 2 46 0 11 | Mut_9 52 8 44 5 35 6 44 1 53 0 12 | Mut_10 55 10 43 7 27 6 42 4 59 0 13 | Mut_11 33 8 38 7 52 10 68 3 45 0 14 | Mut_12 33 4 55 4 44 13 50 0 62 0 15 | Mut_13 47 10 48 7 47 7 54 0 54 0 16 | Mut_14 40 4 53 9 44 12 42 3 38 0 17 | Mut_15 40 8 38 7 37 8 54 3 48 0 18 | Mut_16 47 7 44 5 46 9 55 1 35 0 19 | Mut_17 43 7 48 11 44 8 55 0 46 0 20 | Mut_18 39 10 48 8 43 11 39 4 53 0 21 | Mut_19 52 9 40 4 43 6 42 5 65 0 22 | Mut_20 48 16 38 10 41 9 49 0 47 0 23 | Mut_21 47 12 38 4 33 3 57 3 48 0 24 | Mut_22 34 5 40 4 48 14 35 1 50 0 25 | Mut_23 42 13 46 1 49 9 44 2 47 0 26 | Mut_24 47 7 32 6 46 9 42 4 54 0 27 | Mut_25 43 0 44 0 52 1 49 2 55 0 28 | Mut_26 54 0 47 0 54 3 39 4 57 0 29 | Mut_27 49 1 37 0 38 3 40 4 64 0 30 | Mut_28 53 0 51 0 52 0 50 6 46 0 31 | Mut_29 59 0 59 0 43 2 39 6 52 0 32 | Mut_30 67 0 57 0 50 1 43 8 42 0 33 | Mut_31 36 1 39 0 46 0 50 7 53 0 34 | Mut_32 47 0 55 0 46 2 49 3 42 0 35 | Mut_33 34 0 40 0 44 4 41 6 52 0 36 | Mut_34 44 0 48 0 44 1 40 4 39 0 37 | Mut_35 55 0 39 0 47 5 54 2 37 0 38 | Mut_36 52 0 47 0 38 5 44 6 54 0 39 | Mut_37 59 0 51 0 54 0 48 5 46 0 40 | Mut_38 50 0 58 0 42 6 49 7 42 0 41 | Mut_39 46 1 44 0 49 2 47 3 58 0 42 | Mut_40 41 0 49 0 52 1 48 4 59 0 43 | Mut_41 46 0 48 0 47 1 46 5 45 0 44 | Mut_42 45 1 49 0 46 0 44 8 47 0 45 | Mut_43 52 0 35 0 34 1 45 7 49 0 46 | Mut_44 42 1 50 0 42 1 43 4 34 0 47 | Mut_45 44 0 51 0 67 0 44 4 47 0 48 | Mut_46 35 0 41 0 47 4 36 5 60 0 49 | Mut_47 46 0 42 0 48 2 47 7 48 0 50 | Mut_48 52 0 53 0 52 3 36 3 49 0 51 | Mut_49 42 0 41 0 46 2 51 5 41 0 52 | Mut_50 40 1 49 0 65 0 44 5 53 0 53 | Mut_51 57 0 44 0 49 3 45 8 45 0 54 | Mut_52 38 0 46 0 55 3 46 8 60 0 55 | Mut_53 44 0 51 0 39 5 37 6 40 0 56 | Mut_54 47 0 49 0 44 3 35 2 44 0 57 | Mut_55 47 1 60 0 47 3 39 2 51 0 58 | Mut_56 43 0 47 0 37 3 51 2 55 0 59 | Mut_57 50 0 40 0 40 1 54 4 45 0 60 | Mut_58 43 0 43 0 46 1 48 4 56 0 61 | Mut_59 58 0 52 0 61 3 30 5 48 0 62 | Mut_60 41 10 28 27 45 14 32 10 41 4 63 | Mut_61 34 12 28 23 41 19 35 22 65 7 64 | Mut_62 33 8 16 17 36 12 34 17 50 3 65 | Mut_63 43 17 27 12 45 13 41 15 55 5 66 | Mut_64 35 11 30 21 46 13 32 23 37 3 67 | Mut_65 25 8 34 22 34 14 33 12 50 2 68 | Mut_66 39 17 22 28 42 10 34 23 53 1 69 | Mut_67 47 13 23 17 43 12 37 14 42 1 70 | Mut_68 36 12 25 18 31 9 25 18 44 1 71 | Mut_69 44 19 24 22 32 10 31 19 50 3 72 | Mut_70 37 14 24 28 22 6 37 14 36 1 73 | Mut_71 27 13 29 24 34 13 32 21 39 2 74 | Mut_72 31 9 28 19 31 10 30 23 51 1 75 | Mut_73 42 4 44 0 54 0 31 3 45 0 76 | Mut_74 51 5 43 0 63 0 48 5 42 0 77 | Mut_75 48 5 44 0 49 0 56 4 48 0 78 | Mut_76 41 8 34 15 36 10 53 1 46 0 79 | Mut_77 47 11 45 22 43 10 48 0 54 0 80 | Mut_78 37 9 39 13 31 13 59 5 45 0 81 | Mut_79 34 9 36 8 51 9 51 1 72 0 82 | Mut_80 39 5 34 15 34 2 57 2 60 0 83 | Mut_81 42 9 28 13 45 7 44 0 49 0 84 | Mut_82 52 0 43 0 46 0 48 9 43 0 85 | Mut_83 48 0 46 0 27 0 39 9 55 0 86 | Mut_84 48 0 55 0 55 0 36 4 58 0 87 | Mut_85 53 4 45 0 49 1 51 0 34 0 88 | Mut_86 46 5 46 0 46 2 42 0 44 0 89 | Mut_87 39 4 54 0 47 4 51 0 33 0 90 | Mut_88 49 2 52 0 56 5 56 0 51 0 91 | Mut_89 37 2 55 0 44 0 49 0 41 0 92 | Mut_90 42 1 46 0 45 1 56 0 42 0 93 | Mut_91 53 3 67 0 47 2 44 0 47 0 94 | Mut_92 41 3 39 0 47 1 48 0 54 0 95 | Mut_93 52 0 44 4 43 0 54 0 41 2 96 | Mut_94 55 0 51 2 43 0 47 0 50 3 97 | Mut_95 41 0 59 5 49 0 55 0 45 2 98 | Mut_96 45 0 48 2 46 0 42 0 40 6 99 | Mut_97 45 0 55 2 47 0 51 0 52 1 100 | Mut_98 45 0 52 2 35 0 42 0 50 5 101 | Mut_99 55 0 44 4 49 0 48 0 49 5 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_7.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 45 0 54 7 56 1 40 0 58 0 3 | Mut_1 50 0 50 8 60 9 50 0 48 0 4 | Mut_2 50 0 45 3 58 4 45 0 59 0 5 | Mut_3 50 0 32 5 58 3 52 0 44 0 6 | Mut_4 52 2 37 5 55 3 42 0 42 8 7 | Mut_5 53 5 41 10 41 3 55 0 50 10 8 | Mut_6 53 4 34 6 43 2 40 0 38 10 9 | Mut_7 63 4 39 9 42 0 44 0 40 7 10 | Mut_8 43 4 40 8 39 0 51 0 32 7 11 | Mut_9 57 3 50 0 55 0 52 0 45 13 12 | Mut_10 58 4 51 0 41 0 51 0 27 4 13 | Mut_11 35 3 52 0 57 0 49 0 30 8 14 | Mut_12 49 4 44 0 60 0 51 0 50 11 15 | Mut_13 47 2 62 0 37 0 60 0 41 5 16 | Mut_14 52 3 50 0 54 0 47 0 39 6 17 | Mut_15 45 2 41 0 51 0 49 0 39 6 18 | Mut_16 43 0 44 0 39 0 41 0 28 6 19 | Mut_17 44 4 44 0 46 0 56 0 54 5 20 | Mut_18 52 8 56 0 38 3 41 0 39 4 21 | Mut_19 47 2 50 0 46 4 47 0 39 5 22 | Mut_20 43 2 42 0 46 4 40 0 54 2 23 | Mut_21 45 4 55 0 54 4 54 0 43 1 24 | Mut_22 46 3 41 0 40 6 46 0 43 4 25 | Mut_23 48 2 49 0 36 8 44 0 42 2 26 | Mut_24 47 1 47 0 31 9 56 0 48 3 27 | Mut_25 46 2 42 0 33 2 51 0 50 3 28 | Mut_26 41 5 28 0 44 6 53 0 40 3 29 | Mut_27 31 5 44 0 39 3 61 0 50 5 30 | Mut_28 45 5 49 0 49 5 54 0 62 2 31 | Mut_29 44 3 51 0 51 5 52 0 39 2 32 | Mut_30 47 5 56 0 52 5 52 0 43 3 33 | Mut_31 48 3 53 0 36 8 50 0 41 2 34 | Mut_32 43 7 46 0 45 4 70 0 23 4 35 | Mut_33 45 2 40 0 50 4 44 0 40 4 36 | Mut_34 48 6 34 0 45 12 57 0 38 3 37 | Mut_35 51 4 40 0 54 8 58 0 39 4 38 | Mut_36 55 1 45 0 55 1 48 0 42 2 39 | Mut_37 46 6 61 0 43 14 38 0 47 4 40 | Mut_38 43 1 41 0 44 7 44 0 44 0 41 | Mut_39 49 3 39 0 34 7 36 0 40 2 42 | Mut_40 54 2 51 0 50 10 43 0 47 2 43 | Mut_41 46 3 45 0 46 5 54 0 50 2 44 | Mut_42 56 5 51 0 32 2 69 0 45 3 45 | Mut_43 53 3 51 0 46 3 66 0 32 2 46 | Mut_44 41 3 36 0 60 1 60 0 42 2 47 | Mut_45 60 3 34 0 47 10 47 0 59 1 48 | Mut_46 55 1 64 0 58 6 56 0 52 3 49 | Mut_47 44 1 52 0 42 4 49 0 51 3 50 | Mut_48 40 6 54 0 48 8 55 0 46 0 51 | Mut_49 37 5 42 18 51 4 62 0 35 12 52 | Mut_50 48 6 38 11 49 5 50 0 34 17 53 | Mut_51 36 6 32 9 40 4 58 0 33 12 54 | Mut_52 39 4 50 14 51 2 55 0 23 16 55 | Mut_53 53 7 32 11 47 5 64 0 37 23 56 | Mut_54 37 11 47 10 50 6 47 0 41 20 57 | Mut_55 22 5 38 12 61 5 53 0 33 13 58 | Mut_56 37 6 33 9 38 3 54 0 33 17 59 | Mut_57 38 6 61 0 50 1 64 0 48 3 60 | Mut_58 55 4 52 0 36 2 33 0 39 8 61 | Mut_59 40 6 41 0 53 2 56 0 38 6 62 | Mut_60 50 3 45 0 33 0 52 0 45 7 63 | Mut_61 44 0 54 0 46 4 49 0 50 4 64 | Mut_62 42 3 51 0 53 0 54 0 35 11 65 | Mut_63 48 2 62 0 62 0 45 0 40 7 66 | Mut_64 44 3 46 6 66 1 48 0 46 9 67 | Mut_65 53 4 49 3 52 1 54 0 47 12 68 | Mut_66 49 2 44 5 52 0 54 0 46 7 69 | Mut_67 59 0 42 7 47 2 45 0 49 6 70 | Mut_68 54 5 37 5 51 1 48 0 49 11 71 | Mut_69 30 6 42 3 40 2 48 0 45 7 72 | Mut_70 47 3 43 9 44 3 48 0 55 8 73 | Mut_71 46 5 36 3 52 2 54 0 49 8 74 | Mut_72 53 4 50 8 50 4 44 0 50 5 75 | Mut_73 47 2 41 5 52 1 69 0 46 8 76 | Mut_74 41 2 38 7 48 0 45 0 54 10 77 | Mut_75 44 1 39 7 43 1 50 0 40 2 78 | Mut_76 26 25 40 24 25 19 43 15 23 15 79 | Mut_77 34 16 17 21 27 18 42 5 28 22 80 | Mut_78 30 22 28 26 39 20 40 5 29 15 81 | Mut_79 19 30 28 14 24 16 39 10 37 14 82 | Mut_80 21 18 28 16 27 21 46 9 43 11 83 | Mut_81 19 22 24 15 31 18 37 9 38 25 84 | Mut_82 30 27 33 19 21 21 44 7 38 13 85 | Mut_83 24 18 28 25 27 27 33 7 24 33 86 | Mut_84 19 24 27 15 28 31 52 7 32 16 87 | Mut_85 60 0 56 0 37 13 40 8 52 0 88 | Mut_86 52 0 49 0 47 17 34 5 66 0 89 | Mut_87 37 0 49 0 37 14 46 6 65 0 90 | Mut_88 49 0 48 1 42 11 44 9 47 0 91 | Mut_89 48 0 45 1 36 12 62 6 48 0 92 | Mut_90 47 0 41 1 40 13 37 5 60 0 93 | Mut_91 71 0 42 0 44 11 37 7 38 0 94 | Mut_92 57 0 56 0 38 11 54 7 37 0 95 | Mut_93 50 0 53 0 43 17 42 4 50 0 96 | Mut_94 22 26 49 11 30 18 39 12 33 11 97 | Mut_95 29 31 37 10 26 17 46 6 34 21 98 | Mut_96 23 23 38 14 30 19 51 7 27 13 99 | Mut_97 25 18 41 13 22 26 52 9 36 22 100 | Mut_98 24 26 42 11 26 21 40 9 29 30 101 | Mut_99 28 21 47 10 20 15 42 8 27 20 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_4.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 43 1 51 0 54 2 37 12 43 0 3 | Mut_1 54 0 51 0 55 4 51 7 35 0 4 | Mut_2 35 10 41 0 55 0 43 0 39 13 5 | Mut_3 39 10 62 0 43 0 41 0 36 9 6 | Mut_4 41 12 60 0 56 0 70 0 47 10 7 | Mut_5 49 7 50 0 46 0 63 0 40 8 8 | Mut_6 42 4 51 0 37 0 46 0 37 10 9 | Mut_7 42 10 49 0 57 0 52 0 49 10 10 | Mut_8 39 0 29 0 54 2 40 11 31 0 11 | Mut_9 55 0 47 0 40 3 41 6 43 0 12 | Mut_10 56 0 39 1 51 0 45 11 52 0 13 | Mut_11 52 0 53 6 37 0 35 9 43 0 14 | Mut_12 44 0 31 8 48 0 48 7 38 0 15 | Mut_13 58 0 50 5 49 0 41 12 46 0 16 | Mut_14 44 0 56 5 49 0 34 4 62 0 17 | Mut_15 46 0 38 8 39 0 41 7 42 0 18 | Mut_16 45 0 32 7 45 0 43 11 49 0 19 | Mut_17 47 0 43 6 51 0 39 10 60 0 20 | Mut_18 49 0 34 6 49 0 46 10 51 0 21 | Mut_19 52 0 35 7 42 0 35 11 56 0 22 | Mut_20 60 0 48 7 59 0 38 13 46 0 23 | Mut_21 40 0 46 7 62 0 35 9 58 0 24 | Mut_22 61 0 44 8 60 0 39 6 41 0 25 | Mut_23 60 0 42 3 47 0 38 8 45 0 26 | Mut_24 55 0 44 8 55 0 39 6 54 0 27 | Mut_25 55 0 49 5 66 0 35 15 68 0 28 | Mut_26 50 0 49 4 48 0 44 9 53 0 29 | Mut_27 45 0 42 7 43 0 32 9 48 0 30 | Mut_28 34 0 40 3 50 0 39 8 53 0 31 | Mut_29 51 0 47 9 55 0 43 8 56 0 32 | Mut_30 44 0 39 6 66 0 36 8 53 0 33 | Mut_31 47 0 38 4 43 0 44 4 49 0 34 | Mut_32 32 28 30 12 40 0 50 0 32 9 35 | Mut_33 39 26 43 9 50 0 50 0 34 10 36 | Mut_34 30 23 38 16 59 0 43 0 34 8 37 | Mut_35 28 18 39 11 50 0 57 0 52 15 38 | Mut_36 29 24 35 11 64 0 55 0 34 10 39 | Mut_37 33 26 44 12 40 0 40 0 43 6 40 | Mut_38 35 27 34 9 61 0 58 0 38 11 41 | Mut_39 29 13 36 13 59 0 50 0 47 7 42 | Mut_40 26 15 42 8 55 0 50 0 34 3 43 | Mut_41 26 20 40 12 47 0 56 0 42 8 44 | Mut_42 26 22 35 10 46 0 48 0 44 4 45 | Mut_43 23 18 39 12 58 0 58 0 41 4 46 | Mut_44 24 29 39 15 53 0 54 0 38 7 47 | Mut_45 33 17 34 15 56 0 38 0 35 14 48 | Mut_46 25 20 32 5 53 0 43 0 38 9 49 | Mut_47 24 19 46 13 47 0 43 0 37 10 50 | Mut_48 27 14 35 13 51 0 51 0 45 6 51 | Mut_49 28 15 36 11 58 0 55 0 39 8 52 | Mut_50 21 16 47 13 50 0 42 0 43 11 53 | Mut_51 29 25 48 15 57 0 55 0 54 8 54 | Mut_52 34 18 37 3 51 0 40 0 43 10 55 | Mut_53 27 25 36 13 56 0 50 0 38 6 56 | Mut_54 32 20 38 12 49 0 53 0 31 8 57 | Mut_55 24 20 46 10 49 0 40 0 43 4 58 | Mut_56 21 27 36 4 52 0 49 0 43 11 59 | Mut_57 38 20 49 11 55 0 60 0 50 6 60 | Mut_58 30 30 42 7 49 0 35 0 42 9 61 | Mut_59 37 29 35 9 45 0 42 0 51 7 62 | Mut_60 37 19 30 7 56 0 55 0 34 9 63 | Mut_61 33 23 44 20 51 0 43 0 47 7 64 | Mut_62 25 22 48 13 58 0 47 0 41 13 65 | Mut_63 36 14 49 14 55 0 51 0 39 9 66 | Mut_64 46 20 34 9 46 0 52 0 39 4 67 | Mut_65 31 18 36 15 44 0 34 0 41 10 68 | Mut_66 15 23 37 8 56 0 53 0 51 12 69 | Mut_67 30 16 37 12 44 0 48 0 41 4 70 | Mut_68 35 21 40 6 53 0 47 0 51 8 71 | Mut_69 28 23 47 12 56 0 59 0 42 9 72 | Mut_70 24 17 36 14 37 0 50 0 43 6 73 | Mut_71 24 22 35 14 53 0 44 0 28 3 74 | Mut_72 33 10 41 4 55 0 48 0 45 12 75 | Mut_73 35 16 30 16 40 0 52 0 46 7 76 | Mut_74 57 1 46 0 51 0 26 16 59 3 77 | Mut_75 53 1 50 0 56 4 31 20 40 3 78 | Mut_76 64 0 63 0 46 4 36 12 49 1 79 | Mut_77 46 1 53 0 38 0 36 21 46 5 80 | Mut_78 50 1 39 0 49 2 41 15 40 9 81 | Mut_79 52 1 41 0 37 0 46 13 50 4 82 | Mut_80 58 0 49 0 42 1 46 11 45 2 83 | Mut_81 41 2 39 0 41 3 33 11 51 3 84 | Mut_82 47 0 53 0 44 4 40 9 36 4 85 | Mut_83 24 15 36 25 52 2 32 18 31 16 86 | Mut_84 36 17 29 21 45 2 27 28 33 17 87 | Mut_85 30 21 30 15 48 3 26 17 33 16 88 | Mut_86 28 20 36 16 40 1 22 26 37 8 89 | Mut_87 29 17 36 20 43 3 24 28 29 12 90 | Mut_88 59 0 42 0 38 0 45 0 44 2 91 | Mut_89 56 0 45 0 42 0 51 0 50 3 92 | Mut_90 43 0 59 0 42 0 39 0 53 3 93 | Mut_91 48 0 52 0 50 0 50 0 40 2 94 | Mut_92 52 0 40 0 44 0 49 0 38 3 95 | Mut_93 53 2 61 0 52 0 54 0 52 5 96 | Mut_94 54 0 43 0 52 0 47 0 47 4 97 | Mut_95 44 0 35 0 43 0 50 0 52 2 98 | Mut_96 36 1 48 0 57 0 50 6 43 0 99 | Mut_97 57 0 46 0 43 0 31 3 46 0 100 | Mut_98 45 0 53 0 50 0 46 12 56 0 101 | Mut_99 51 0 57 0 58 0 30 7 51 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_2.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 48 0 44 0 42 4 60 0 53 3 3 | Mut_1 52 0 58 0 45 1 43 0 47 6 4 | Mut_2 37 0 56 0 46 2 57 0 45 8 5 | Mut_3 52 0 44 0 51 1 50 0 46 3 6 | Mut_4 57 0 34 0 57 2 65 0 53 7 7 | Mut_5 52 0 47 0 46 2 51 0 44 5 8 | Mut_6 53 0 61 0 54 3 60 0 40 6 9 | Mut_7 65 0 56 0 53 3 48 0 60 4 10 | Mut_8 58 0 42 0 49 0 49 0 53 5 11 | Mut_9 50 0 68 0 55 0 52 0 50 6 12 | Mut_10 57 0 43 0 41 2 57 0 37 6 13 | Mut_11 50 0 52 0 50 1 58 0 49 7 14 | Mut_12 47 0 54 0 61 1 49 0 42 3 15 | Mut_13 47 0 46 0 44 0 41 0 40 2 16 | Mut_14 39 0 43 0 46 5 53 0 39 3 17 | Mut_15 34 0 59 0 47 4 68 0 42 4 18 | Mut_16 61 0 49 0 33 6 51 0 53 7 19 | Mut_17 51 0 50 0 55 3 31 0 31 9 20 | Mut_18 50 0 44 0 48 2 60 0 38 9 21 | Mut_19 58 0 54 0 40 1 42 0 51 4 22 | Mut_20 46 0 48 0 49 5 40 0 40 7 23 | Mut_21 66 0 46 0 54 0 57 0 44 4 24 | Mut_22 47 0 52 0 43 7 60 0 53 3 25 | Mut_23 38 0 40 0 47 5 43 0 37 7 26 | Mut_24 53 0 50 0 47 0 52 0 35 7 27 | Mut_25 44 0 45 0 62 2 51 0 43 9 28 | Mut_26 54 0 52 0 52 2 46 0 51 4 29 | Mut_27 42 0 50 0 43 2 59 0 52 2 30 | Mut_28 34 1 25 26 52 1 47 9 26 20 31 | Mut_29 56 3 36 24 50 1 40 10 30 18 32 | Mut_30 37 1 37 17 54 1 37 12 36 18 33 | Mut_31 55 3 28 17 48 1 49 11 29 18 34 | Mut_32 47 1 22 8 52 0 31 8 26 16 35 | Mut_33 49 3 32 14 57 0 48 14 36 15 36 | Mut_34 49 2 34 17 54 0 35 13 40 17 37 | Mut_35 50 3 20 19 45 0 40 13 34 17 38 | Mut_36 41 2 28 18 62 1 37 14 38 16 39 | Mut_37 57 6 21 19 57 0 53 13 25 15 40 | Mut_38 46 0 40 19 47 0 36 12 28 19 41 | Mut_39 56 4 50 12 50 0 32 15 26 22 42 | Mut_40 34 3 26 18 51 1 49 13 58 11 43 | Mut_41 58 6 21 10 49 4 50 15 33 17 44 | Mut_42 42 6 46 20 44 1 44 9 26 12 45 | Mut_43 45 3 36 16 46 0 42 20 41 13 46 | Mut_44 38 0 50 0 40 0 44 0 40 7 47 | Mut_45 57 0 43 0 52 0 47 0 31 4 48 | Mut_46 53 0 51 0 48 0 46 0 33 9 49 | Mut_47 47 0 40 10 59 0 56 4 52 0 50 | Mut_48 54 0 44 11 45 0 46 4 52 0 51 | Mut_49 61 0 24 17 56 0 43 2 61 0 52 | Mut_50 42 0 23 16 58 0 57 3 35 0 53 | Mut_51 52 0 30 20 41 0 50 2 58 0 54 | Mut_52 52 0 44 15 42 0 43 3 43 0 55 | Mut_53 61 0 30 21 46 0 49 1 49 0 56 | Mut_54 44 0 35 23 60 0 51 2 55 0 57 | Mut_55 58 0 37 21 46 0 38 4 54 0 58 | Mut_56 51 0 33 19 54 0 48 1 62 0 59 | Mut_57 57 0 39 20 46 0 69 5 52 0 60 | Mut_58 57 0 31 13 39 0 57 4 48 0 61 | Mut_59 44 0 37 26 66 0 38 5 47 0 62 | Mut_60 60 0 40 14 47 0 56 2 44 0 63 | Mut_61 38 0 40 15 53 0 41 3 49 0 64 | Mut_62 56 0 41 19 51 0 48 2 48 0 65 | Mut_63 69 0 28 18 43 0 48 1 47 0 66 | Mut_64 50 0 34 18 47 0 48 3 58 0 67 | Mut_65 59 0 53 0 35 15 51 0 55 0 68 | Mut_66 43 0 43 0 44 10 48 0 54 0 69 | Mut_67 54 0 54 0 36 12 51 0 57 1 70 | Mut_68 50 0 41 0 25 14 54 0 50 1 71 | Mut_69 53 0 65 0 37 10 44 0 52 0 72 | Mut_70 38 0 60 0 26 13 59 0 38 0 73 | Mut_71 55 0 55 0 39 25 44 0 60 1 74 | Mut_72 44 0 61 0 39 20 51 0 51 1 75 | Mut_73 47 1 29 26 39 16 42 13 28 23 76 | Mut_74 46 4 43 16 34 20 42 6 29 17 77 | Mut_75 48 5 26 13 32 28 37 6 24 27 78 | Mut_76 45 1 41 22 31 15 46 15 28 19 79 | Mut_77 61 1 36 16 41 21 31 13 21 20 80 | Mut_78 40 1 32 19 38 19 40 12 26 17 81 | Mut_79 39 4 27 16 30 19 36 17 33 22 82 | Mut_80 59 2 43 20 30 11 47 18 30 24 83 | Mut_81 50 5 28 17 24 23 47 15 33 22 84 | Mut_82 46 1 43 11 17 22 36 12 30 29 85 | Mut_83 52 6 27 11 30 18 41 9 33 25 86 | Mut_84 56 3 32 21 30 18 40 8 23 23 87 | Mut_85 60 1 31 9 38 18 43 9 29 15 88 | Mut_86 49 4 21 13 34 16 29 12 33 27 89 | Mut_87 46 3 24 11 28 16 29 10 24 27 90 | Mut_88 48 1 38 18 31 20 39 13 27 21 91 | Mut_89 51 2 27 14 23 14 31 12 26 18 92 | Mut_90 59 0 51 0 33 0 50 3 61 1 93 | Mut_91 39 0 54 0 48 0 41 4 47 3 94 | Mut_92 51 0 59 0 47 0 48 3 52 4 95 | Mut_93 50 0 57 0 35 0 51 5 37 2 96 | Mut_94 42 0 54 0 45 1 44 4 40 0 97 | Mut_95 54 0 40 0 47 0 33 5 46 0 98 | Mut_96 48 0 67 0 39 0 48 8 45 0 99 | Mut_97 46 0 55 0 49 1 58 10 52 0 100 | Mut_98 45 0 55 0 48 2 49 7 42 0 101 | Mut_99 32 0 42 0 52 1 43 5 40 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_0.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 45 0 69 0 49 4 48 0 44 8 3 | Mut_1 59 0 58 0 52 3 58 0 46 3 4 | Mut_2 34 0 44 0 46 2 49 0 49 8 5 | Mut_3 57 0 48 0 43 1 55 0 52 5 6 | Mut_4 55 0 55 0 47 2 56 0 36 7 7 | Mut_5 58 0 54 0 46 2 57 0 48 6 8 | Mut_6 48 0 53 0 47 0 53 0 50 6 9 | Mut_7 48 0 48 0 60 2 59 0 33 6 10 | Mut_8 47 0 45 0 47 4 28 0 34 19 11 | Mut_9 43 0 63 0 48 2 45 0 34 10 12 | Mut_10 42 0 53 0 56 2 56 0 43 8 13 | Mut_11 47 5 37 10 43 14 44 2 37 5 14 | Mut_12 37 6 45 5 47 11 33 2 35 7 15 | Mut_13 41 3 36 9 36 20 45 3 35 12 16 | Mut_14 49 4 39 9 42 15 51 1 37 6 17 | Mut_15 45 3 33 6 37 12 41 1 33 15 18 | Mut_16 39 1 47 7 38 9 48 2 37 11 19 | Mut_17 39 4 53 8 31 8 60 3 40 12 20 | Mut_18 43 8 35 7 40 7 52 5 32 15 21 | Mut_19 58 3 44 9 37 9 35 1 37 9 22 | Mut_20 41 5 50 7 42 9 53 4 48 10 23 | Mut_21 54 3 25 7 34 9 45 5 40 11 24 | Mut_22 42 3 45 2 46 0 46 0 60 0 25 | Mut_23 53 1 55 8 45 0 54 0 47 0 26 | Mut_24 55 2 46 3 56 0 51 0 55 0 27 | Mut_25 51 4 42 4 59 0 50 0 54 0 28 | Mut_26 46 5 49 4 43 0 56 0 55 0 29 | Mut_27 52 6 38 3 64 0 59 0 62 0 30 | Mut_28 39 3 43 5 47 0 67 0 41 0 31 | Mut_29 54 3 47 3 49 0 52 0 28 0 32 | Mut_30 53 4 49 6 47 0 57 0 67 0 33 | Mut_31 43 3 39 6 57 0 43 0 58 0 34 | Mut_32 37 2 44 5 45 0 45 0 36 0 35 | Mut_33 52 2 39 6 52 0 38 0 43 0 36 | Mut_34 43 7 43 4 54 0 52 0 52 0 37 | Mut_35 46 2 43 8 58 0 47 0 59 0 38 | Mut_36 50 1 47 3 49 0 50 0 45 0 39 | Mut_37 41 3 53 4 51 0 50 0 48 0 40 | Mut_38 52 9 37 2 40 0 44 0 36 0 41 | Mut_39 44 3 43 3 56 0 43 0 46 0 42 | Mut_40 53 3 36 3 45 0 54 0 49 0 43 | Mut_41 42 5 48 3 48 0 50 0 50 0 44 | Mut_42 46 6 43 3 43 0 63 0 65 0 45 | Mut_43 39 3 44 9 39 0 46 0 52 0 46 | Mut_44 40 1 31 4 51 0 52 0 50 0 47 | Mut_45 54 3 38 9 53 0 43 0 55 0 48 | Mut_46 36 0 39 2 56 0 46 0 53 0 49 | Mut_47 48 6 47 8 55 0 37 0 52 0 50 | Mut_48 38 3 59 4 56 0 41 0 57 0 51 | Mut_49 52 0 49 0 45 1 48 3 42 2 52 | Mut_50 59 0 53 0 49 1 46 4 55 5 53 | Mut_51 53 0 52 0 54 3 46 7 34 9 54 | Mut_52 48 0 46 0 43 0 57 4 41 5 55 | Mut_53 48 0 62 0 56 3 43 6 48 5 56 | Mut_54 46 0 57 0 46 1 37 4 40 11 57 | Mut_55 35 4 47 0 58 0 49 7 45 0 58 | Mut_56 43 3 53 2 46 0 46 2 54 0 59 | Mut_57 36 5 44 10 35 15 37 14 33 16 60 | Mut_58 52 11 39 11 37 17 44 14 24 21 61 | Mut_59 35 8 33 8 34 14 30 18 31 22 62 | Mut_60 46 5 37 13 31 20 35 15 34 30 63 | Mut_61 31 7 42 14 28 17 21 14 30 24 64 | Mut_62 46 9 31 12 36 11 33 22 22 26 65 | Mut_63 41 9 34 9 29 15 31 21 22 24 66 | Mut_64 39 6 54 7 31 11 36 13 34 22 67 | Mut_65 43 13 33 8 36 14 28 22 19 31 68 | Mut_66 55 7 42 11 31 12 28 11 25 26 69 | Mut_67 47 4 37 5 32 17 23 24 27 21 70 | Mut_68 45 8 41 6 36 19 26 22 28 15 71 | Mut_69 42 10 37 14 40 12 32 20 21 31 72 | Mut_70 25 9 38 13 26 10 33 18 34 25 73 | Mut_71 44 10 38 11 24 20 26 12 30 29 74 | Mut_72 33 13 39 7 28 18 37 16 28 21 75 | Mut_73 46 7 45 12 35 12 37 25 23 26 76 | Mut_74 50 8 40 12 36 18 23 17 20 24 77 | Mut_75 46 14 33 9 32 15 38 22 27 21 78 | Mut_76 41 7 42 11 39 17 31 12 28 31 79 | Mut_77 41 11 33 12 28 21 21 15 24 21 80 | Mut_78 59 5 33 13 39 26 43 17 28 28 81 | Mut_79 40 6 28 14 30 19 38 18 31 27 82 | Mut_80 38 7 39 11 35 17 26 17 39 16 83 | Mut_81 31 10 33 8 35 16 34 28 22 17 84 | Mut_82 39 9 34 12 28 13 35 8 23 34 85 | Mut_83 24 8 31 4 25 8 26 17 29 25 86 | Mut_84 45 7 43 15 43 11 28 16 39 26 87 | Mut_85 27 7 35 12 33 25 44 25 19 21 88 | Mut_86 30 15 27 10 37 11 33 19 28 25 89 | Mut_87 37 13 32 13 37 13 39 20 24 28 90 | Mut_88 60 0 57 2 46 0 40 5 40 0 91 | Mut_89 59 0 42 3 41 0 41 0 46 0 92 | Mut_90 39 0 52 2 34 0 54 5 39 0 93 | Mut_91 49 0 66 0 36 6 54 3 66 0 94 | Mut_92 56 0 56 0 36 8 50 2 63 0 95 | Mut_93 50 0 40 0 41 10 45 4 37 0 96 | Mut_94 47 0 43 0 43 6 56 6 49 0 97 | Mut_95 51 0 51 0 45 6 41 3 49 0 98 | Mut_96 46 0 50 3 54 0 45 0 29 5 99 | Mut_97 40 0 46 0 54 0 47 0 35 8 100 | Mut_98 76 0 50 5 47 0 38 0 27 10 101 | Mut_99 48 0 49 4 48 0 56 0 36 18 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_3.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 48 6 44 3 48 0 38 0 55 4 3 | Mut_1 38 13 38 9 68 0 46 0 52 6 4 | Mut_2 43 8 35 5 48 0 47 0 48 0 5 | Mut_3 38 7 51 8 49 0 52 0 40 5 6 | Mut_4 54 0 49 3 55 8 40 0 38 0 7 | Mut_5 20 26 42 12 35 12 18 19 33 19 8 | Mut_6 22 41 37 13 28 10 26 22 30 16 9 | Mut_7 19 20 41 16 29 20 27 27 26 17 10 | Mut_8 27 24 38 9 43 14 22 28 41 25 11 | Mut_9 26 22 36 8 27 11 21 21 34 19 12 | Mut_10 22 28 52 14 34 7 17 20 32 25 13 | Mut_11 28 25 32 12 23 20 29 17 40 27 14 | Mut_12 30 21 41 21 27 18 27 25 24 20 15 | Mut_13 23 17 44 11 35 15 17 23 32 18 16 | Mut_14 40 2 45 2 54 0 50 5 35 0 17 | Mut_15 51 3 52 3 40 0 45 6 39 0 18 | Mut_16 49 7 56 1 44 0 47 3 52 0 19 | Mut_17 42 3 43 1 60 0 40 9 31 0 20 | Mut_18 43 1 51 1 44 0 29 5 46 0 21 | Mut_19 51 2 51 2 47 0 57 3 56 0 22 | Mut_20 48 0 50 0 45 0 37 4 40 0 23 | Mut_21 47 1 45 2 62 0 48 6 70 0 24 | Mut_22 49 0 60 0 44 0 43 3 61 0 25 | Mut_23 43 2 53 3 48 0 40 6 41 0 26 | Mut_24 56 1 51 2 40 0 36 8 59 0 27 | Mut_25 39 0 55 1 50 0 39 0 45 0 28 | Mut_26 34 10 41 6 53 5 45 5 37 16 29 | Mut_27 38 16 45 6 45 5 49 6 29 21 30 | Mut_28 35 8 48 8 45 5 62 7 32 15 31 | Mut_29 45 13 43 8 40 9 49 1 38 21 32 | Mut_30 42 10 41 13 58 8 45 3 33 18 33 | Mut_31 24 10 42 9 43 5 54 7 28 20 34 | Mut_32 36 13 47 12 52 5 46 4 31 12 35 | Mut_33 33 9 40 9 55 5 25 6 37 24 36 | Mut_34 42 8 38 8 54 6 34 6 35 28 37 | Mut_35 29 8 51 9 46 3 34 4 19 21 38 | Mut_36 31 13 51 0 57 0 42 3 54 0 39 | Mut_37 37 9 53 0 52 0 46 7 46 0 40 | Mut_38 38 12 51 0 47 0 46 7 38 0 41 | Mut_39 27 12 48 0 43 0 42 8 54 0 42 | Mut_40 39 8 52 0 50 0 51 4 45 0 43 | Mut_41 36 18 49 0 54 0 34 4 50 0 44 | Mut_42 36 9 41 0 50 0 40 5 47 0 45 | Mut_43 40 14 46 0 49 0 57 6 54 0 46 | Mut_44 41 16 61 0 50 0 41 6 40 0 47 | Mut_45 41 14 58 0 46 0 61 11 53 0 48 | Mut_46 31 13 52 0 54 0 44 6 51 0 49 | Mut_47 32 14 45 0 46 0 63 6 50 0 50 | Mut_48 42 14 59 0 50 0 45 6 60 0 51 | Mut_49 33 8 50 0 56 0 37 9 51 0 52 | Mut_50 48 11 51 0 51 0 40 7 54 0 53 | Mut_51 32 16 54 0 45 0 48 7 52 0 54 | Mut_52 36 16 55 0 61 0 46 8 57 0 55 | Mut_53 51 21 47 0 43 0 42 5 56 0 56 | Mut_54 44 2 43 0 48 0 45 0 40 17 57 | Mut_55 37 1 45 0 61 0 45 0 42 15 58 | Mut_56 46 5 45 0 50 0 59 0 39 13 59 | Mut_57 53 2 58 0 56 0 49 0 42 11 60 | Mut_58 47 0 65 0 50 0 45 0 34 10 61 | Mut_59 48 2 51 0 53 0 48 0 43 17 62 | Mut_60 46 2 46 0 51 0 50 0 38 7 63 | Mut_61 45 1 50 0 55 0 42 0 40 15 64 | Mut_62 43 2 56 0 47 0 42 0 44 11 65 | Mut_63 59 0 46 5 54 5 56 0 51 3 66 | Mut_64 53 0 54 0 53 5 47 0 43 2 67 | Mut_65 57 0 49 0 36 4 40 0 39 4 68 | Mut_66 49 0 50 2 44 5 53 0 34 0 69 | Mut_67 51 0 48 1 51 6 57 0 45 5 70 | Mut_68 48 0 58 2 48 3 47 0 49 6 71 | Mut_69 53 0 49 0 55 4 60 0 47 4 72 | Mut_70 46 0 44 1 53 4 50 0 55 8 73 | Mut_71 63 0 41 3 61 0 40 0 50 5 74 | Mut_72 45 0 44 0 49 1 33 7 56 0 75 | Mut_73 52 0 42 0 55 4 35 14 62 0 76 | Mut_74 43 0 50 0 44 2 45 10 50 0 77 | Mut_75 60 0 63 0 53 4 34 14 40 0 78 | Mut_76 49 0 34 0 44 2 36 19 50 0 79 | Mut_77 48 0 48 0 36 1 37 15 43 0 80 | Mut_78 56 0 53 0 53 1 43 12 50 0 81 | Mut_79 40 0 57 0 53 0 32 13 54 0 82 | Mut_80 51 0 48 0 30 3 36 15 45 0 83 | Mut_81 38 0 37 0 44 1 35 8 43 0 84 | Mut_82 53 0 55 0 49 4 39 15 53 0 85 | Mut_83 42 0 62 0 61 2 39 11 50 0 86 | Mut_84 53 0 54 0 45 2 40 14 49 0 87 | Mut_85 46 0 50 0 58 1 41 10 38 0 88 | Mut_86 37 11 38 17 43 9 38 4 35 22 89 | Mut_87 39 7 37 14 31 11 45 4 23 20 90 | Mut_88 29 13 49 11 35 14 33 11 32 20 91 | Mut_89 40 13 29 11 33 11 38 4 32 23 92 | Mut_90 36 10 41 7 36 14 41 7 25 17 93 | Mut_91 38 10 33 10 37 7 40 5 38 20 94 | Mut_92 42 5 43 12 46 17 44 2 35 24 95 | Mut_93 44 12 33 6 34 10 41 5 26 18 96 | Mut_94 40 14 44 13 18 9 42 6 31 18 97 | Mut_95 39 6 25 13 28 12 35 8 32 15 98 | Mut_96 34 8 32 15 37 16 50 7 26 19 99 | Mut_97 30 9 37 10 37 15 44 13 33 25 100 | Mut_98 45 12 34 17 35 15 52 12 31 19 101 | Mut_99 27 9 36 8 38 9 43 6 31 23 102 | -------------------------------------------------------------------------------- /src/probcomparison.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * probcomparison.cpp 3 | * 4 | * Created on: 26-mar-2015 5 | * Author: M. El-Kebir 6 | */ 7 | 8 | #include "probcomparison.h" 9 | 10 | #include 11 | #include 12 | 13 | namespace vaff { 14 | 15 | ProbComparison::ProbComparison(const AncestryMatrix& A, 16 | const MaxSolution::Triple& solution) 17 | : _A(A) 18 | , _solution(solution) 19 | , _toMutationsFromSol() 20 | , _toSolCluster() 21 | { 22 | constructMappings(); 23 | determinePairs(); 24 | } 25 | 26 | void ProbComparison::constructMappings() 27 | { 28 | typedef std::vector StringVector; 29 | typedef StringVector::const_iterator StringVectorIt; 30 | 31 | int n = _solution._F.getNrCols(); 32 | 33 | _toMutationsFromSol = StlIntMatrix(n, StlIntVector()); 34 | _toSolCluster = StlIntVector(_A.getNrRows(), -1); 35 | 36 | for (int j = 0; j < n; ++j) 37 | { 38 | StringVector s; 39 | boost::split(s, _solution._F.getColLabel(j), boost::is_any_of(";")); 40 | 41 | for (StringVectorIt it2 = s.begin(); it2 != s.end(); ++it2) 42 | { 43 | if (*it2 != "") 44 | { 45 | int org_j = boost::lexical_cast(*it2); 46 | 47 | _toMutationsFromSol[j].push_back(org_j); 48 | _toSolCluster[org_j] = j; 49 | } 50 | } 51 | } 52 | } 53 | 54 | void ProbComparison::determinePairs() 55 | { 56 | int org_j = 0; 57 | for (StlIntVectorIt it_1 = _toSolCluster.begin(); 58 | it_1 != _toSolCluster.end(); ++it_1, ++org_j) 59 | { 60 | int j = *it_1; 61 | if (j == -1) continue; 62 | 63 | int org_k = org_j + 1; 64 | for (StlIntVectorIt it_2 = it_1 + 1; 65 | it_2 != _toSolCluster.end(); ++it_2, ++org_k) 66 | { 67 | int k = *it_2; 68 | if (k == -1) continue; 69 | 70 | if (j == k) 71 | { 72 | _clustered.insert(std::make_pair(std::min(org_j, org_k), 73 | std::max(org_j, org_k))); 74 | } 75 | else 76 | { 77 | if (_solution._T.ancestral(j, k)) 78 | { 79 | _ancestral.insert(std::make_pair(org_j, org_k)); 80 | } 81 | else if (_solution._T.ancestral(k, j)) 82 | { 83 | _ancestral.insert(std::make_pair(org_k, org_j)); 84 | } 85 | else 86 | { 87 | assert(_solution._T.incomparable(j, k)); 88 | _incomparable.insert(std::make_pair(std::min(org_j, org_k), 89 | std::max(org_j, org_k))); 90 | } 91 | } 92 | } 93 | } 94 | } 95 | 96 | StlDoubleVector ProbComparison::clustered() const 97 | { 98 | typedef StlIntPairSet::const_iterator StlIntPairSetIt; 99 | 100 | StlDoubleVector res; 101 | for (StlIntPairSetIt it = _clustered.begin(); 102 | it != _clustered.end(); ++it) 103 | { 104 | res.push_back(_A(it->first, it->second)); 105 | res.push_back(_A(it->second, it->first)); 106 | } 107 | return res; 108 | } 109 | 110 | StlDoubleVector ProbComparison::ancestral() const 111 | { 112 | typedef StlIntPairSet::const_iterator StlIntPairSetIt; 113 | 114 | StlDoubleVector res; 115 | for (StlIntPairSetIt it = _ancestral.begin(); 116 | it != _ancestral.end(); ++it) 117 | { 118 | res.push_back(_A(it->first, it->second)); 119 | } 120 | return res; 121 | } 122 | 123 | StlDoubleVector ProbComparison::incomparable() const 124 | { 125 | typedef StlIntPairSet::const_iterator StlIntPairSetIt; 126 | 127 | StlDoubleVector res; 128 | for (StlIntPairSetIt it = _incomparable.begin(); 129 | it != _incomparable.end(); ++it) 130 | { 131 | res.push_back(_A(it->first, it->second)); 132 | res.push_back(_A(it->second, it->first)); 133 | } 134 | return res; 135 | } 136 | 137 | } // namespace vaff -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_8.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 51 0 68 0 46 7 42 0 57 0 3 | Mut_1 50 0 49 0 53 7 46 0 61 0 4 | Mut_2 45 0 52 0 34 4 54 0 57 0 5 | Mut_3 59 0 34 0 56 5 57 0 39 0 6 | Mut_4 35 16 45 6 37 10 31 18 44 8 7 | Mut_5 25 12 32 7 44 11 26 14 42 8 8 | Mut_6 43 7 38 17 38 19 24 9 54 9 9 | Mut_7 40 8 26 14 48 18 39 20 49 8 10 | Mut_8 39 8 45 11 29 13 39 17 33 4 11 | Mut_9 37 10 27 12 32 12 30 25 50 7 12 | Mut_10 29 11 45 10 30 18 34 12 50 6 13 | Mut_11 42 12 40 8 39 17 25 18 40 4 14 | Mut_12 37 10 43 7 37 12 29 12 46 5 15 | Mut_13 27 10 40 6 28 11 32 13 36 8 16 | Mut_14 43 13 42 13 28 6 40 22 41 6 17 | Mut_15 44 10 41 8 28 12 35 16 41 7 18 | Mut_16 32 17 46 6 42 7 41 16 41 5 19 | Mut_17 34 10 54 6 39 18 40 17 42 3 20 | Mut_18 41 10 37 7 46 13 29 19 44 7 21 | Mut_19 44 0 46 5 55 1 36 11 63 0 22 | Mut_20 56 0 36 10 34 4 34 13 43 0 23 | Mut_21 42 0 40 9 60 1 36 18 43 0 24 | Mut_22 51 0 55 7 34 1 30 16 34 0 25 | Mut_23 41 0 40 10 59 3 41 9 44 0 26 | Mut_24 48 0 47 1 42 6 31 15 59 0 27 | Mut_25 41 0 38 12 44 13 34 14 52 0 28 | Mut_26 34 0 44 6 60 1 32 19 38 0 29 | Mut_27 54 0 39 7 45 11 25 17 51 0 30 | Mut_28 44 0 55 10 42 9 19 12 38 0 31 | Mut_29 43 0 48 11 38 9 36 13 57 0 32 | Mut_30 49 0 42 8 35 10 33 25 40 0 33 | Mut_31 64 0 35 8 50 6 30 17 38 0 34 | Mut_32 54 0 36 9 56 9 33 17 47 0 35 | Mut_33 39 0 43 9 47 11 32 8 47 0 36 | Mut_34 56 0 42 8 39 7 32 12 63 0 37 | Mut_35 40 14 41 13 38 12 28 22 41 4 38 | Mut_36 34 16 36 13 33 10 39 19 39 4 39 | Mut_37 36 10 57 16 34 16 34 13 45 10 40 | Mut_38 35 15 45 10 36 8 36 18 40 5 41 | Mut_39 40 11 38 14 34 15 37 10 30 7 42 | Mut_40 39 17 45 12 30 20 33 21 53 5 43 | Mut_41 40 20 39 7 33 12 28 17 38 9 44 | Mut_42 37 6 34 14 39 13 38 13 40 6 45 | Mut_43 35 19 37 10 36 12 36 18 50 11 46 | Mut_44 38 19 36 7 29 15 29 17 38 5 47 | Mut_45 44 19 35 18 32 20 36 13 38 4 48 | Mut_46 37 12 36 10 24 12 52 16 38 7 49 | Mut_47 33 11 45 8 43 7 41 24 55 5 50 | Mut_48 35 9 30 9 32 11 22 20 53 4 51 | Mut_49 29 21 46 6 34 18 26 19 49 6 52 | Mut_50 38 9 45 11 51 19 38 14 42 7 53 | Mut_51 35 15 42 13 31 9 30 15 52 5 54 | Mut_52 39 17 38 4 44 19 29 17 32 4 55 | Mut_53 39 12 47 12 40 18 30 16 49 3 56 | Mut_54 52 10 43 13 36 14 33 19 58 6 57 | Mut_55 47 12 41 8 31 16 36 18 44 8 58 | Mut_56 46 14 35 10 34 19 35 23 46 3 59 | Mut_57 39 9 46 10 39 16 33 16 55 4 60 | Mut_58 36 12 46 14 41 13 32 21 54 5 61 | Mut_59 52 0 51 0 45 0 63 0 46 4 62 | Mut_60 53 0 48 0 60 0 35 0 42 11 63 | Mut_61 54 1 40 0 46 0 51 0 39 10 64 | Mut_62 52 1 53 0 67 0 47 0 39 8 65 | Mut_63 39 0 48 0 44 0 55 0 42 8 66 | Mut_64 54 1 45 0 49 0 59 0 49 10 67 | Mut_65 42 0 48 0 50 0 49 0 47 7 68 | Mut_66 59 0 47 0 58 0 49 0 42 6 69 | Mut_67 57 0 58 0 52 0 50 0 25 7 70 | Mut_68 51 0 51 0 45 0 54 0 46 10 71 | Mut_69 47 0 53 0 48 0 49 0 40 5 72 | Mut_70 46 0 56 0 48 0 57 0 39 11 73 | Mut_71 53 0 49 0 54 0 48 0 48 11 74 | Mut_72 59 0 49 0 43 0 49 0 29 4 75 | Mut_73 53 1 44 0 63 0 52 0 38 6 76 | Mut_74 55 0 66 0 48 0 41 0 46 12 77 | Mut_75 37 0 45 0 46 0 58 0 47 6 78 | Mut_76 41 0 48 0 43 0 57 0 52 7 79 | Mut_77 59 0 43 0 60 0 56 0 45 8 80 | Mut_78 48 0 43 0 56 0 51 0 52 6 81 | Mut_79 60 0 46 0 44 0 47 0 35 10 82 | Mut_80 65 0 39 0 50 0 43 0 33 7 83 | Mut_81 54 2 35 5 47 0 50 0 52 0 84 | Mut_82 55 1 57 2 56 0 56 0 47 0 85 | Mut_83 55 0 37 5 30 0 46 0 55 0 86 | Mut_84 54 1 52 1 48 0 50 0 48 0 87 | Mut_85 46 0 44 3 47 0 49 0 49 0 88 | Mut_86 42 0 48 4 51 0 63 0 62 0 89 | Mut_87 52 1 51 5 51 0 48 0 55 0 90 | Mut_88 49 2 51 1 56 0 55 0 49 0 91 | Mut_89 64 0 50 2 43 0 49 0 54 0 92 | Mut_90 46 1 54 2 48 0 44 0 43 0 93 | Mut_91 50 0 56 3 39 0 45 0 46 0 94 | Mut_92 49 1 39 1 55 0 43 0 52 0 95 | Mut_93 44 0 46 1 62 0 41 0 48 0 96 | Mut_94 38 12 39 11 39 16 25 11 32 13 97 | Mut_95 30 7 25 15 43 16 29 18 36 15 98 | Mut_96 29 21 20 27 29 14 26 23 37 14 99 | Mut_97 48 15 22 28 34 9 23 25 48 12 100 | Mut_98 33 22 23 28 38 12 19 28 30 9 101 | Mut_99 32 13 24 15 32 16 20 23 28 8 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_1.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 44 7 45 4 37 0 45 2 44 0 3 | Mut_1 42 3 58 5 53 0 34 0 54 0 4 | Mut_2 35 9 54 5 58 0 49 1 49 0 5 | Mut_3 44 10 45 1 48 0 44 1 59 0 6 | Mut_4 42 13 52 0 52 0 53 4 45 0 7 | Mut_5 36 4 46 3 44 0 45 0 46 0 8 | Mut_6 46 5 53 4 52 0 51 1 45 0 9 | Mut_7 35 5 49 5 52 0 65 1 54 0 10 | Mut_8 45 6 49 4 56 0 61 2 47 0 11 | Mut_9 44 2 42 0 53 0 43 2 51 0 12 | Mut_10 44 7 46 3 49 0 38 0 59 0 13 | Mut_11 41 8 32 2 37 0 53 5 48 0 14 | Mut_12 42 7 51 2 68 0 46 1 52 0 15 | Mut_13 32 9 58 2 69 0 47 3 49 0 16 | Mut_14 46 6 51 4 54 0 44 3 68 0 17 | Mut_15 45 0 33 0 45 0 46 4 49 0 18 | Mut_16 43 0 53 4 56 0 45 5 51 0 19 | Mut_17 56 0 43 1 65 0 38 2 54 0 20 | Mut_18 57 0 61 1 49 0 47 6 58 0 21 | Mut_19 58 0 50 5 61 0 40 8 53 0 22 | Mut_20 55 0 58 4 52 0 42 3 51 0 23 | Mut_21 57 0 47 3 65 0 37 10 39 0 24 | Mut_22 33 0 47 3 57 0 45 2 49 0 25 | Mut_23 55 1 38 11 45 3 52 5 43 10 26 | Mut_24 44 0 43 6 52 6 43 4 40 13 27 | Mut_25 41 5 28 11 27 12 47 2 47 6 28 | Mut_26 44 1 45 20 38 15 49 3 34 9 29 | Mut_27 34 7 31 20 43 20 41 2 47 8 30 | Mut_28 45 5 32 11 39 16 50 4 43 8 31 | Mut_29 38 6 32 6 33 22 41 6 38 8 32 | Mut_30 54 11 38 19 38 16 44 7 47 12 33 | Mut_31 45 5 34 7 48 17 53 5 43 8 34 | Mut_32 50 5 39 21 31 16 50 6 41 6 35 | Mut_33 38 4 37 12 29 22 51 5 43 12 36 | Mut_34 46 5 31 18 35 18 47 2 54 9 37 | Mut_35 35 3 30 14 38 16 46 3 34 8 38 | Mut_36 47 3 21 16 35 26 45 5 49 5 39 | Mut_37 47 3 34 8 42 11 38 3 38 4 40 | Mut_38 52 11 27 18 29 9 52 5 46 7 41 | Mut_39 30 32 25 19 39 22 46 10 28 32 42 | Mut_40 31 23 22 22 15 23 30 11 30 18 43 | Mut_41 23 24 38 16 20 38 33 6 24 15 44 | Mut_42 26 20 41 27 22 17 38 5 38 17 45 | Mut_43 34 27 30 22 21 21 40 5 21 23 46 | Mut_44 21 33 30 19 27 24 51 12 27 18 47 | Mut_45 26 17 31 20 30 20 38 9 32 26 48 | Mut_46 24 21 39 17 36 24 38 6 31 27 49 | Mut_47 29 19 22 13 31 23 44 4 33 18 50 | Mut_48 26 22 27 23 34 27 35 8 20 29 51 | Mut_49 17 25 36 15 21 23 42 9 25 21 52 | Mut_50 16 17 41 23 32 24 32 5 24 22 53 | Mut_51 37 22 43 19 23 31 52 6 29 18 54 | Mut_52 32 27 42 24 28 22 48 3 39 24 55 | Mut_53 28 27 34 14 27 20 42 3 27 10 56 | Mut_54 25 25 20 21 33 23 38 9 27 27 57 | Mut_55 40 19 28 16 21 31 40 0 37 26 58 | Mut_56 36 27 33 13 29 23 44 9 29 13 59 | Mut_57 18 31 37 12 33 21 47 5 33 15 60 | Mut_58 26 31 35 16 30 25 59 10 35 14 61 | Mut_59 26 24 38 12 27 19 40 4 22 27 62 | Mut_60 26 10 26 13 33 18 43 10 30 27 63 | Mut_61 20 23 27 17 28 24 44 7 40 19 64 | Mut_62 28 27 32 22 26 21 50 6 26 19 65 | Mut_63 19 26 36 23 20 22 47 10 36 19 66 | Mut_64 22 21 36 18 32 23 49 5 25 17 67 | Mut_65 30 21 31 13 24 28 41 4 38 27 68 | Mut_66 26 19 28 26 23 21 44 4 27 14 69 | Mut_67 29 22 29 21 22 31 31 13 39 23 70 | Mut_68 33 26 29 17 25 25 46 10 30 15 71 | Mut_69 25 17 37 16 28 29 42 3 33 17 72 | Mut_70 63 0 47 11 47 4 56 7 39 6 73 | Mut_71 52 0 42 7 31 2 51 7 45 5 74 | Mut_72 55 0 32 12 42 2 47 4 48 2 75 | Mut_73 61 0 31 17 49 5 44 4 48 10 76 | Mut_74 54 0 30 9 37 5 40 2 41 3 77 | Mut_75 39 12 59 0 40 0 42 0 31 18 78 | Mut_76 26 4 60 0 41 0 57 0 42 8 79 | Mut_77 45 10 41 0 46 0 62 0 28 9 80 | Mut_78 40 20 51 0 43 0 35 0 30 14 81 | Mut_79 40 12 48 0 45 0 46 0 47 9 82 | Mut_80 31 6 49 0 50 0 56 0 41 9 83 | Mut_81 43 8 46 0 51 0 48 0 36 6 84 | Mut_82 44 15 52 0 49 0 44 0 34 14 85 | Mut_83 40 17 64 0 41 0 42 0 35 8 86 | Mut_84 47 16 50 0 57 0 68 0 37 10 87 | Mut_85 36 12 42 0 54 0 44 0 40 11 88 | Mut_86 39 6 43 0 42 0 54 0 43 12 89 | Mut_87 43 12 61 0 43 0 53 0 26 10 90 | Mut_88 48 15 31 0 44 0 57 0 43 8 91 | Mut_89 36 13 55 0 38 0 54 0 42 10 92 | Mut_90 37 12 48 0 44 0 61 0 37 9 93 | Mut_91 40 15 60 0 51 0 41 0 37 7 94 | Mut_92 43 7 46 0 37 0 37 0 32 13 95 | Mut_93 35 6 55 0 34 0 62 0 38 13 96 | Mut_94 47 5 38 4 49 10 45 0 47 0 97 | Mut_95 36 4 41 5 31 14 45 0 46 0 98 | Mut_96 42 10 49 0 59 0 38 0 36 10 99 | Mut_97 30 13 44 0 43 0 42 0 35 12 100 | Mut_98 35 12 54 0 42 0 44 0 41 11 101 | Mut_99 60 0 35 10 56 3 68 0 41 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_50_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_5.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 17 22 44 21 28 22 20 18 31 21 3 | Mut_1 22 26 34 18 34 28 32 16 18 24 4 | Mut_2 25 24 41 22 31 26 28 18 19 26 5 | Mut_3 33 30 34 20 20 30 21 25 28 27 6 | Mut_4 29 25 42 11 20 21 38 22 27 25 7 | Mut_5 32 19 38 20 30 33 31 17 24 22 8 | Mut_6 26 28 29 19 15 21 25 17 20 25 9 | Mut_7 36 5 56 0 51 1 28 20 44 1 10 | Mut_8 52 4 50 0 40 0 33 14 43 0 11 | Mut_9 43 5 55 0 50 1 41 18 58 1 12 | Mut_10 39 6 45 0 43 1 40 18 58 3 13 | Mut_11 47 5 56 0 54 0 27 15 57 0 14 | Mut_12 40 6 54 0 44 0 38 20 42 2 15 | Mut_13 41 3 55 0 46 1 39 17 44 0 16 | Mut_14 19 24 26 12 27 22 26 16 23 21 17 | Mut_15 24 25 38 25 21 24 24 21 21 23 18 | Mut_16 27 19 42 11 26 30 24 20 25 12 19 | Mut_17 32 27 37 15 26 22 33 17 25 22 20 | Mut_18 29 18 30 15 16 20 24 15 28 22 21 | Mut_19 21 30 41 25 25 32 32 18 14 29 22 | Mut_20 59 0 39 14 43 9 42 0 35 0 23 | Mut_21 43 0 35 17 38 10 53 0 58 0 24 | Mut_22 45 0 33 19 43 11 62 0 52 0 25 | Mut_23 50 0 34 18 37 9 55 0 46 0 26 | Mut_24 48 3 51 0 46 0 50 0 36 16 27 | Mut_25 49 1 54 0 52 0 47 0 29 21 28 | Mut_26 40 8 56 0 55 0 50 1 36 21 29 | Mut_27 51 3 49 0 51 0 50 0 31 18 30 | Mut_28 40 5 56 0 45 0 61 1 29 18 31 | Mut_29 50 6 46 0 57 0 42 0 29 16 32 | Mut_30 46 3 47 0 53 0 48 0 42 12 33 | Mut_31 43 5 46 0 45 0 58 0 29 24 34 | Mut_32 54 7 63 0 46 0 60 2 39 10 35 | Mut_33 48 5 37 0 64 0 50 0 29 26 36 | Mut_34 36 5 61 0 60 0 48 0 29 21 37 | Mut_35 34 2 55 0 55 0 45 0 27 21 38 | Mut_36 49 4 63 0 57 0 51 0 30 27 39 | Mut_37 57 6 41 0 61 0 62 0 30 10 40 | Mut_38 49 1 55 0 59 0 41 0 56 0 41 | Mut_39 46 2 62 0 58 0 49 0 49 0 42 | Mut_40 43 3 51 0 57 0 36 0 46 0 43 | Mut_41 48 2 43 0 54 1 44 0 54 0 44 | Mut_42 44 0 35 0 61 0 49 0 56 0 45 | Mut_43 60 1 46 0 37 0 51 0 50 0 46 | Mut_44 60 0 45 0 54 0 46 0 41 0 47 | Mut_45 25 27 41 0 35 15 51 0 29 21 48 | Mut_46 36 25 45 2 34 7 45 0 41 16 49 | Mut_47 31 20 52 3 38 11 59 0 30 19 50 | Mut_48 28 13 51 0 31 13 46 1 22 20 51 | Mut_49 38 16 41 1 45 6 49 0 27 24 52 | Mut_50 28 19 61 0 35 12 47 1 30 24 53 | Mut_51 25 21 39 0 38 8 53 0 27 28 54 | Mut_52 36 19 46 2 34 10 43 0 34 20 55 | Mut_53 39 13 41 1 41 12 48 0 25 14 56 | Mut_54 30 22 48 3 30 15 53 0 28 21 57 | Mut_55 29 18 51 2 32 15 52 0 23 22 58 | Mut_56 29 18 46 2 39 7 51 0 32 24 59 | Mut_57 30 17 46 0 35 6 58 0 28 19 60 | Mut_58 31 17 45 0 47 10 50 0 18 20 61 | Mut_59 42 22 48 0 41 11 57 0 41 18 62 | Mut_60 29 19 43 3 43 16 50 0 37 25 63 | Mut_61 27 18 55 0 31 10 35 1 31 21 64 | Mut_62 33 25 69 2 45 8 48 1 33 22 65 | Mut_63 40 12 43 3 40 7 58 0 25 27 66 | Mut_64 31 22 37 0 33 11 56 0 32 17 67 | Mut_65 32 8 48 1 36 7 47 0 27 19 68 | Mut_66 28 13 55 2 52 11 51 0 33 23 69 | Mut_67 34 20 54 0 33 11 53 0 29 26 70 | Mut_68 27 23 48 3 33 6 45 0 29 13 71 | Mut_69 29 15 49 0 36 14 49 0 31 19 72 | Mut_70 41 25 47 0 45 6 52 0 25 18 73 | Mut_71 34 26 56 1 41 11 59 0 25 21 74 | Mut_72 27 16 60 0 33 12 47 0 28 27 75 | Mut_73 35 25 51 1 39 14 48 0 28 11 76 | Mut_74 23 18 47 1 42 8 48 0 20 19 77 | Mut_75 50 5 59 0 52 0 55 1 35 15 78 | Mut_76 44 8 54 0 46 0 43 0 29 26 79 | Mut_77 40 4 59 0 47 0 63 0 24 17 80 | Mut_78 44 5 44 0 47 0 56 0 29 15 81 | Mut_79 34 6 40 0 46 0 45 0 27 24 82 | Mut_80 36 5 52 0 54 0 54 1 29 29 83 | Mut_81 45 3 39 0 43 0 32 0 31 19 84 | Mut_82 46 5 50 0 49 0 46 1 23 19 85 | Mut_83 41 2 52 0 55 0 45 0 32 18 86 | Mut_84 48 5 49 0 43 0 41 0 31 21 87 | Mut_85 59 7 44 0 53 0 49 0 31 14 88 | Mut_86 54 10 63 0 44 0 36 0 19 23 89 | Mut_87 42 4 53 0 47 0 47 0 30 20 90 | Mut_88 66 0 35 16 40 13 38 0 48 0 91 | Mut_89 30 19 49 0 23 13 53 0 53 0 92 | Mut_90 28 21 61 0 34 14 54 0 39 1 93 | Mut_91 39 14 47 0 29 8 51 0 43 1 94 | Mut_92 35 13 51 0 49 16 51 0 46 3 95 | Mut_93 39 16 51 0 45 10 55 0 44 3 96 | Mut_94 46 17 68 0 39 13 46 0 47 2 97 | Mut_95 39 11 56 0 47 13 44 0 40 0 98 | Mut_96 35 10 69 0 52 13 46 0 55 0 99 | Mut_97 32 12 44 0 42 16 51 0 60 0 100 | Mut_98 32 16 47 0 39 15 52 0 55 4 101 | Mut_99 32 14 45 0 34 12 66 0 58 1 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_6.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 99 0 105 1 75 22 87 15 57 38 3 | Mut_1 99 0 117 4 77 17 70 20 43 52 4 | Mut_2 92 0 97 4 81 28 76 17 51 54 5 | Mut_3 117 0 91 2 74 27 85 18 51 44 6 | Mut_4 103 0 95 0 80 24 79 11 46 48 7 | Mut_5 105 0 99 2 53 22 88 20 60 39 8 | Mut_6 99 1 96 0 100 0 73 0 94 0 9 | Mut_7 109 1 97 0 91 0 97 0 105 0 10 | Mut_8 114 0 93 3 98 0 117 0 101 0 11 | Mut_9 110 4 97 2 95 0 100 0 96 0 12 | Mut_10 98 0 94 1 95 0 95 0 102 0 13 | Mut_11 106 1 94 0 109 0 104 0 96 0 14 | Mut_12 100 2 97 0 110 0 86 0 95 0 15 | Mut_13 104 0 91 2 104 0 115 0 109 0 16 | Mut_14 80 0 101 3 107 0 99 0 107 0 17 | Mut_15 97 1 88 0 108 0 103 0 91 0 18 | Mut_16 101 0 101 4 114 0 102 0 86 0 19 | Mut_17 102 1 101 2 96 0 102 0 93 0 20 | Mut_18 105 0 102 2 111 0 103 0 79 0 21 | Mut_19 92 0 99 3 95 0 103 0 107 0 22 | Mut_20 96 0 87 3 99 0 96 0 84 0 23 | Mut_21 103 1 97 3 106 0 109 0 91 0 24 | Mut_22 96 0 99 2 113 0 114 0 118 0 25 | Mut_23 116 0 60 45 106 0 92 10 98 0 26 | Mut_24 93 0 65 36 100 0 100 8 98 0 27 | Mut_25 115 0 55 45 106 0 103 16 82 0 28 | Mut_26 115 0 73 30 104 0 88 10 94 1 29 | Mut_27 112 0 61 44 103 0 80 18 106 0 30 | Mut_28 106 0 68 43 79 0 104 9 91 0 31 | Mut_29 94 0 98 0 99 0 69 24 77 4 32 | Mut_30 112 0 105 0 106 0 91 27 96 1 33 | Mut_31 113 0 110 0 109 0 85 20 92 3 34 | Mut_32 103 0 103 0 104 0 86 11 86 6 35 | Mut_33 110 0 101 0 87 0 87 25 101 5 36 | Mut_34 94 0 112 0 90 0 79 27 99 5 37 | Mut_35 103 0 105 0 83 0 80 20 96 6 38 | Mut_36 84 0 86 0 105 0 87 11 92 2 39 | Mut_37 108 0 99 0 85 0 90 19 103 4 40 | Mut_38 87 0 103 0 103 0 85 24 82 6 41 | Mut_39 99 0 88 0 113 0 69 21 93 2 42 | Mut_40 89 0 104 0 107 0 86 15 103 2 43 | Mut_41 94 0 102 0 94 0 87 11 77 5 44 | Mut_42 102 0 85 0 114 0 84 17 96 1 45 | Mut_43 108 0 100 0 108 0 86 27 100 2 46 | Mut_44 99 0 75 0 104 0 66 13 103 4 47 | Mut_45 87 0 109 0 96 0 62 29 81 7 48 | Mut_46 100 0 107 0 108 0 69 18 100 4 49 | Mut_47 89 0 91 0 100 0 74 18 95 1 50 | Mut_48 106 0 100 0 112 0 76 24 86 2 51 | Mut_49 125 0 100 0 100 0 68 25 101 3 52 | Mut_50 87 0 110 0 88 15 105 6 89 0 53 | Mut_51 108 0 102 0 93 16 87 5 79 0 54 | Mut_52 94 0 89 0 67 15 78 7 98 0 55 | Mut_53 111 0 103 0 75 7 97 1 112 0 56 | Mut_54 93 0 115 0 87 17 78 2 114 0 57 | Mut_55 110 0 116 0 86 14 112 4 98 0 58 | Mut_56 94 0 98 0 91 10 85 5 117 0 59 | Mut_57 81 0 97 0 92 9 88 3 107 0 60 | Mut_58 100 0 96 0 86 11 89 4 112 0 61 | Mut_59 91 0 102 0 78 12 82 7 88 0 62 | Mut_60 89 0 103 0 83 16 90 5 105 0 63 | Mut_61 89 0 100 0 84 13 72 4 100 0 64 | Mut_62 112 0 104 0 92 15 80 1 111 0 65 | Mut_63 99 0 104 0 96 9 95 3 91 0 66 | Mut_64 121 0 99 0 92 12 91 1 88 0 67 | Mut_65 95 0 88 0 93 11 107 2 121 0 68 | Mut_66 97 0 89 0 89 5 80 4 86 0 69 | Mut_67 104 0 94 0 80 9 97 3 112 0 70 | Mut_68 101 0 88 0 94 19 80 4 109 0 71 | Mut_69 113 0 83 0 80 13 91 3 113 0 72 | Mut_70 109 0 99 0 77 12 96 3 106 0 73 | Mut_71 84 0 139 0 106 20 84 7 94 0 74 | Mut_72 103 0 103 0 96 7 85 2 94 0 75 | Mut_73 114 0 103 0 89 18 92 7 109 0 76 | Mut_74 110 0 96 0 97 20 84 6 98 0 77 | Mut_75 105 0 86 0 80 11 89 6 98 0 78 | Mut_76 115 0 80 0 76 15 100 1 84 0 79 | Mut_77 100 0 77 0 93 15 98 6 95 0 80 | Mut_78 106 0 110 0 95 8 92 3 95 0 81 | Mut_79 94 0 87 0 90 15 109 4 95 0 82 | Mut_80 117 0 102 0 91 7 94 8 112 0 83 | Mut_81 81 0 105 0 89 6 97 4 89 0 84 | Mut_82 81 0 96 0 76 12 90 6 92 0 85 | Mut_83 117 0 121 0 70 8 94 3 90 0 86 | Mut_84 92 0 104 0 89 18 97 0 112 0 87 | Mut_85 112 0 98 0 84 13 107 6 105 0 88 | Mut_86 103 0 84 0 77 11 96 5 94 0 89 | Mut_87 81 14 112 1 79 22 73 25 52 39 90 | Mut_88 71 29 51 48 63 21 63 32 65 59 91 | Mut_89 107 0 108 0 73 27 93 0 73 42 92 | Mut_90 61 31 52 36 49 37 64 25 37 46 93 | Mut_91 74 26 62 44 49 42 53 27 46 60 94 | Mut_92 74 36 55 38 44 40 71 30 45 50 95 | Mut_93 108 0 94 1 99 0 83 0 91 9 96 | Mut_94 111 0 110 7 87 1 99 0 91 7 97 | Mut_95 102 0 77 4 80 1 103 0 83 16 98 | Mut_96 95 0 110 1 107 0 82 0 99 10 99 | Mut_97 87 0 90 4 102 0 103 0 103 14 100 | Mut_98 80 0 101 4 92 1 89 0 96 14 101 | Mut_99 121 0 96 2 99 0 84 0 97 9 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_2.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 91 0 98 0 89 4 112 0 92 8 3 | Mut_1 103 0 110 0 95 2 109 0 80 9 4 | Mut_2 113 0 79 0 81 5 111 0 79 18 5 | Mut_3 99 0 100 0 108 8 96 0 83 13 6 | Mut_4 82 0 113 0 84 5 95 0 94 9 7 | Mut_5 92 0 106 0 94 4 101 0 84 8 8 | Mut_6 96 0 91 0 97 3 119 0 77 7 9 | Mut_7 84 0 96 0 73 4 107 0 88 11 10 | Mut_8 95 0 120 0 89 3 107 0 73 7 11 | Mut_9 100 0 94 0 77 3 96 0 85 11 12 | Mut_10 110 0 100 0 109 12 88 0 92 6 13 | Mut_11 94 0 82 0 84 5 102 0 98 10 14 | Mut_12 111 0 109 0 93 8 103 0 82 13 15 | Mut_13 94 0 97 0 94 5 89 0 86 10 16 | Mut_14 104 0 99 0 86 2 110 0 88 10 17 | Mut_15 93 0 113 0 106 6 103 0 83 15 18 | Mut_16 95 0 93 0 97 7 93 0 103 11 19 | Mut_17 94 0 106 0 101 7 97 0 81 9 20 | Mut_18 94 0 97 0 90 4 109 0 106 10 21 | Mut_19 91 0 89 0 89 9 110 0 104 13 22 | Mut_20 98 0 99 0 100 4 96 0 108 12 23 | Mut_21 100 0 83 0 65 4 84 0 80 6 24 | Mut_22 109 0 106 0 94 5 119 0 100 12 25 | Mut_23 95 0 108 0 87 4 94 0 73 12 26 | Mut_24 86 0 92 0 95 4 94 0 76 14 27 | Mut_25 95 0 108 0 93 2 75 0 92 10 28 | Mut_26 100 0 98 0 93 5 89 0 96 9 29 | Mut_27 109 0 107 0 101 6 122 0 77 6 30 | Mut_28 88 4 63 29 107 2 67 26 59 34 31 | Mut_29 94 5 61 34 110 0 82 28 65 30 32 | Mut_30 70 3 59 22 90 1 87 31 59 28 33 | Mut_31 87 3 62 34 105 2 61 28 62 49 34 | Mut_32 82 6 59 42 112 0 79 13 79 42 35 | Mut_33 93 5 68 36 115 2 75 26 64 38 36 | Mut_34 110 3 47 29 98 5 90 20 68 32 37 | Mut_35 110 2 81 39 108 1 59 20 68 33 38 | Mut_36 87 5 72 37 108 3 88 34 75 26 39 | Mut_37 98 5 54 26 105 1 75 20 68 38 40 | Mut_38 89 3 55 42 105 1 78 20 63 30 41 | Mut_39 104 5 59 31 98 1 72 31 80 43 42 | Mut_40 72 5 57 36 107 2 72 32 70 21 43 | Mut_41 75 2 57 32 93 1 56 28 54 39 44 | Mut_42 90 6 62 42 98 1 88 28 78 37 45 | Mut_43 103 3 50 36 87 2 77 29 56 39 46 | Mut_44 99 0 103 0 96 4 88 0 87 10 47 | Mut_45 94 0 119 0 91 0 112 0 81 11 48 | Mut_46 86 6 95 0 97 0 97 0 82 35 49 | Mut_47 93 0 72 30 98 0 96 5 113 0 50 | Mut_48 117 0 67 25 85 0 98 2 113 0 51 | Mut_49 117 0 51 36 101 0 81 5 100 0 52 | Mut_50 97 0 67 28 89 0 96 5 123 0 53 | Mut_51 103 0 66 24 101 0 92 3 97 0 54 | Mut_52 96 0 62 45 108 0 88 2 91 0 55 | Mut_53 91 0 59 38 94 0 93 5 91 0 56 | Mut_54 93 0 75 31 98 0 118 5 104 0 57 | Mut_55 106 0 52 34 106 0 96 4 95 0 58 | Mut_56 93 0 74 32 101 0 100 5 112 0 59 | Mut_57 116 0 57 46 107 0 97 8 86 0 60 | Mut_58 118 0 68 34 98 0 111 2 108 0 61 | Mut_59 97 0 64 39 106 0 83 6 86 0 62 | Mut_60 94 0 67 33 91 0 70 5 106 0 63 | Mut_61 118 0 66 35 102 0 97 8 107 0 64 | Mut_62 97 0 71 38 112 0 96 2 88 0 65 | Mut_63 106 0 68 30 129 0 78 4 92 0 66 | Mut_64 120 0 65 34 82 0 90 2 86 0 67 | Mut_65 90 0 104 0 80 27 107 0 84 3 68 | Mut_66 86 0 85 0 78 32 101 0 86 1 69 | Mut_67 105 0 106 0 74 19 100 0 92 1 70 | Mut_68 82 0 106 0 75 28 109 0 93 2 71 | Mut_69 96 0 105 0 75 20 96 0 98 5 72 | Mut_70 96 0 100 0 63 16 101 0 85 3 73 | Mut_71 107 0 94 0 74 28 95 0 78 3 74 | Mut_72 111 0 114 0 82 38 96 0 96 0 75 | Mut_73 100 5 61 32 63 35 67 27 55 46 76 | Mut_74 104 2 65 33 77 32 81 18 62 39 77 | Mut_75 92 3 51 24 64 25 76 22 59 43 78 | Mut_76 87 4 63 36 61 37 85 30 51 32 79 | Mut_77 120 7 73 36 67 33 75 11 45 54 80 | Mut_78 91 2 57 34 81 35 74 22 51 47 81 | Mut_79 108 4 80 35 48 20 85 18 45 43 82 | Mut_80 95 3 69 37 77 38 100 27 41 42 83 | Mut_81 80 8 66 39 66 26 90 18 73 45 84 | Mut_82 88 6 62 32 69 37 78 35 69 39 85 | Mut_83 81 5 56 24 71 24 62 32 61 56 86 | Mut_84 81 5 52 39 70 36 70 21 28 43 87 | Mut_85 77 2 67 40 71 32 66 18 57 55 88 | Mut_86 79 6 53 36 71 37 69 18 49 38 89 | Mut_87 93 3 67 24 78 40 84 26 60 45 90 | Mut_88 95 3 57 23 53 33 75 23 64 50 91 | Mut_89 91 9 66 28 59 27 60 27 62 48 92 | Mut_90 110 0 105 0 91 0 85 6 102 3 93 | Mut_91 108 0 108 0 98 0 84 7 108 5 94 | Mut_92 103 0 109 0 97 0 102 11 105 2 95 | Mut_93 105 0 98 0 101 0 99 5 106 0 96 | Mut_94 102 0 95 0 117 3 86 14 87 0 97 | Mut_95 92 0 107 0 121 0 92 17 99 0 98 | Mut_96 94 0 81 0 96 0 81 17 102 0 99 | Mut_97 109 0 109 0 111 2 82 11 109 0 100 | Mut_98 83 0 92 0 89 0 86 15 106 0 101 | Mut_99 100 0 104 0 113 3 87 8 98 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_7.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 94 0 91 18 85 5 95 0 98 0 3 | Mut_1 95 0 89 11 98 3 97 0 104 0 4 | Mut_2 103 0 96 10 79 9 92 0 88 0 5 | Mut_3 98 0 84 11 93 6 116 0 111 0 6 | Mut_4 78 9 95 8 102 9 83 0 68 13 7 | Mut_5 81 9 105 13 88 5 91 0 79 16 8 | Mut_6 110 5 90 7 92 3 83 0 85 19 9 | Mut_7 91 7 101 25 104 6 110 0 87 9 10 | Mut_8 102 5 101 10 92 4 129 0 83 11 11 | Mut_9 95 10 107 0 107 0 98 0 89 26 12 | Mut_10 86 8 96 0 94 0 95 0 84 15 13 | Mut_11 95 11 96 0 83 0 114 0 85 18 14 | Mut_12 85 6 103 0 107 0 86 0 89 10 15 | Mut_13 94 5 125 0 124 0 96 0 82 26 16 | Mut_14 91 8 107 0 91 0 118 0 78 21 17 | Mut_15 81 4 115 0 88 0 105 0 70 17 18 | Mut_16 91 7 114 0 121 0 96 0 77 15 19 | Mut_17 88 3 89 0 101 0 99 0 77 15 20 | Mut_18 91 5 83 0 68 7 96 0 97 10 21 | Mut_19 103 11 93 0 81 12 88 0 78 4 22 | Mut_20 89 4 93 0 92 5 106 0 73 10 23 | Mut_21 97 10 101 0 90 6 86 0 86 4 24 | Mut_22 90 5 77 0 115 8 98 0 90 4 25 | Mut_23 98 9 91 0 96 6 102 0 88 5 26 | Mut_24 87 6 98 0 94 16 121 0 88 1 27 | Mut_25 100 7 99 0 88 14 99 0 107 5 28 | Mut_26 77 8 107 0 91 8 96 0 101 2 29 | Mut_27 102 8 98 0 92 7 100 0 91 2 30 | Mut_28 109 4 114 0 85 7 90 0 95 5 31 | Mut_29 121 6 98 0 90 9 84 0 97 5 32 | Mut_30 95 11 105 0 93 14 115 0 76 5 33 | Mut_31 95 6 82 0 95 10 88 0 76 2 34 | Mut_32 93 6 102 0 82 10 101 0 95 11 35 | Mut_33 84 4 108 0 83 11 87 0 98 5 36 | Mut_34 103 2 99 0 92 15 114 0 105 4 37 | Mut_35 97 6 99 0 75 15 100 0 99 3 38 | Mut_36 103 2 106 0 88 16 117 0 98 5 39 | Mut_37 104 6 91 0 82 16 132 0 103 5 40 | Mut_38 100 9 86 0 96 13 105 0 94 5 41 | Mut_39 89 11 104 0 85 11 112 0 103 4 42 | Mut_40 109 6 77 0 89 12 110 0 94 3 43 | Mut_41 82 7 116 0 72 9 89 0 93 4 44 | Mut_42 97 10 89 0 106 5 81 0 81 9 45 | Mut_43 94 4 104 0 98 11 101 0 85 4 46 | Mut_44 86 11 84 0 82 8 98 0 93 4 47 | Mut_45 94 4 86 0 81 15 104 0 110 6 48 | Mut_46 86 8 112 0 74 19 72 0 86 3 49 | Mut_47 92 5 102 0 100 18 105 0 107 3 50 | Mut_48 98 12 83 0 93 12 97 0 84 6 51 | Mut_49 88 7 73 26 99 7 107 0 59 23 52 | Mut_50 74 19 73 29 96 7 97 0 60 26 53 | Mut_51 85 16 84 15 87 4 93 0 72 26 54 | Mut_52 90 21 63 26 99 4 79 0 67 36 55 | Mut_53 84 12 72 29 80 7 100 0 67 36 56 | Mut_54 97 16 47 13 78 9 93 0 81 37 57 | Mut_55 98 11 64 25 93 12 110 0 68 35 58 | Mut_56 81 16 69 16 86 3 101 0 70 45 59 | Mut_57 84 9 101 0 111 2 108 0 86 17 60 | Mut_58 100 6 118 0 95 2 103 0 74 19 61 | Mut_59 102 13 105 0 91 2 96 0 85 16 62 | Mut_60 101 6 89 0 108 1 90 0 77 17 63 | Mut_61 103 5 104 0 105 2 78 0 73 17 64 | Mut_62 95 8 93 0 92 2 88 0 88 15 65 | Mut_63 90 13 82 0 97 3 85 0 73 14 66 | Mut_64 98 3 85 16 90 1 103 0 70 20 67 | Mut_65 101 10 108 11 89 2 101 0 89 18 68 | Mut_66 92 13 83 6 85 0 101 0 69 17 69 | Mut_67 96 5 87 11 115 2 92 0 66 13 70 | Mut_68 94 2 80 9 101 1 92 0 82 13 71 | Mut_69 100 9 103 6 106 5 92 0 88 12 72 | Mut_70 97 8 84 5 80 4 121 0 97 9 73 | Mut_71 102 4 103 7 97 3 97 0 92 15 74 | Mut_72 87 6 93 10 109 2 99 0 91 15 75 | Mut_73 83 11 87 6 89 3 128 0 72 18 76 | Mut_74 102 8 79 14 86 2 107 0 69 15 77 | Mut_75 91 7 90 12 119 5 97 0 88 16 78 | Mut_76 51 44 57 48 69 45 105 20 68 47 79 | Mut_77 65 49 51 52 45 40 87 21 62 36 80 | Mut_78 59 54 67 47 46 53 70 14 66 35 81 | Mut_79 59 42 63 49 57 49 107 20 74 41 82 | Mut_80 47 32 53 42 60 50 80 17 56 28 83 | Mut_81 61 46 52 41 56 53 104 19 57 44 84 | Mut_82 53 42 57 55 65 38 82 17 72 27 85 | Mut_83 62 56 58 49 55 44 69 9 65 40 86 | Mut_84 58 43 56 41 43 43 95 14 65 37 87 | Mut_85 104 0 90 0 78 34 95 28 92 0 88 | Mut_86 102 0 102 0 72 22 73 19 119 0 89 | Mut_87 107 0 113 0 73 20 77 10 103 0 90 | Mut_88 102 0 106 2 72 34 92 18 71 0 91 | Mut_89 81 0 98 0 87 27 92 22 111 0 92 | Mut_90 101 0 112 0 66 30 79 22 100 0 93 | Mut_91 77 0 89 0 80 34 87 19 92 0 94 | Mut_92 114 0 85 0 69 33 84 12 93 0 95 | Mut_93 100 0 97 0 75 23 93 22 108 0 96 | Mut_94 53 52 71 25 55 56 84 31 67 35 97 | Mut_95 52 45 68 29 69 47 73 22 67 35 98 | Mut_96 49 57 65 13 65 43 75 16 61 45 99 | Mut_97 50 60 73 23 64 34 82 16 67 37 100 | Mut_98 57 52 81 28 51 56 83 11 53 43 101 | Mut_99 52 40 76 30 55 51 91 16 49 32 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_9.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 93 1 99 0 84 6 98 9 87 0 3 | Mut_1 88 17 88 11 82 15 95 1 106 0 4 | Mut_2 76 20 85 13 94 22 92 4 108 0 5 | Mut_3 81 16 83 14 89 22 96 7 101 0 6 | Mut_4 73 18 73 12 87 20 108 8 92 0 7 | Mut_5 97 15 87 10 87 21 96 5 98 0 8 | Mut_6 81 18 102 15 92 15 96 5 86 0 9 | Mut_7 71 13 76 14 77 18 86 1 94 0 10 | Mut_8 70 17 86 10 82 19 97 3 111 0 11 | Mut_9 68 16 88 18 75 21 95 2 69 0 12 | Mut_10 87 15 84 11 93 14 99 6 97 0 13 | Mut_11 83 17 95 13 80 18 123 7 87 0 14 | Mut_12 72 22 102 15 88 15 88 5 112 0 15 | Mut_13 79 13 71 9 87 21 86 3 98 0 16 | Mut_14 76 22 101 12 97 18 119 9 108 0 17 | Mut_15 81 23 99 12 71 19 102 3 129 0 18 | Mut_16 89 21 103 17 81 28 85 8 101 0 19 | Mut_17 71 15 105 11 80 18 95 4 94 0 20 | Mut_18 81 15 89 14 79 14 106 5 84 0 21 | Mut_19 73 12 76 7 59 15 83 2 91 0 22 | Mut_20 87 20 76 10 86 15 90 1 101 0 23 | Mut_21 82 20 79 15 75 22 101 4 109 0 24 | Mut_22 87 17 98 9 62 19 97 5 109 0 25 | Mut_23 72 14 103 11 89 19 98 2 86 0 26 | Mut_24 92 18 84 11 102 22 85 5 90 0 27 | Mut_25 104 1 106 0 109 5 93 11 106 0 28 | Mut_26 85 1 100 0 81 4 74 10 90 0 29 | Mut_27 89 0 91 0 99 4 88 9 75 0 30 | Mut_28 92 2 104 0 91 2 89 10 104 0 31 | Mut_29 101 2 99 0 103 2 94 8 91 0 32 | Mut_30 108 1 94 0 106 6 104 11 101 0 33 | Mut_31 95 0 109 0 96 5 84 15 89 0 34 | Mut_32 105 0 110 0 107 6 83 10 102 0 35 | Mut_33 88 1 95 0 99 6 97 18 99 0 36 | Mut_34 84 0 91 0 109 8 93 13 108 0 37 | Mut_35 82 0 87 0 94 2 104 8 89 0 38 | Mut_36 90 3 104 0 74 7 64 10 104 0 39 | Mut_37 97 1 79 0 81 5 98 8 103 0 40 | Mut_38 92 2 99 0 94 3 94 9 92 0 41 | Mut_39 87 0 84 0 97 7 71 14 126 0 42 | Mut_40 90 0 103 0 85 5 92 17 110 0 43 | Mut_41 105 2 99 0 75 13 82 12 85 0 44 | Mut_42 99 0 99 0 82 3 86 9 90 0 45 | Mut_43 83 1 111 0 94 5 88 11 82 0 46 | Mut_44 92 1 90 0 116 11 92 16 100 0 47 | Mut_45 80 0 101 0 85 3 71 13 109 0 48 | Mut_46 95 2 117 0 102 6 95 10 120 0 49 | Mut_47 98 0 105 0 89 5 77 8 100 0 50 | Mut_48 105 0 80 0 89 3 85 12 86 0 51 | Mut_49 107 3 103 0 87 8 94 18 97 0 52 | Mut_50 109 0 111 0 92 5 88 9 111 0 53 | Mut_51 78 0 87 0 90 5 103 13 86 0 54 | Mut_52 104 1 94 0 103 2 89 15 104 0 55 | Mut_53 101 1 102 0 111 4 78 9 95 0 56 | Mut_54 109 0 114 0 92 6 79 3 92 0 57 | Mut_55 96 1 110 0 86 4 95 7 90 0 58 | Mut_56 92 0 110 0 78 4 104 10 104 0 59 | Mut_57 96 0 100 0 92 3 85 12 99 0 60 | Mut_58 96 0 95 0 101 7 79 8 89 0 61 | Mut_59 109 0 103 0 91 5 84 5 111 0 62 | Mut_60 64 23 59 41 73 29 54 31 82 2 63 | Mut_61 62 31 54 50 74 32 66 31 90 12 64 | Mut_62 89 21 59 47 87 26 65 32 96 3 65 | Mut_63 85 39 50 45 72 31 58 34 104 6 66 | Mut_64 74 31 68 38 72 26 63 49 89 4 67 | Mut_65 86 34 42 52 78 26 65 34 86 5 68 | Mut_66 58 31 63 44 79 26 56 33 108 4 69 | Mut_67 75 27 55 40 75 25 58 32 90 5 70 | Mut_68 49 35 40 45 91 36 51 32 102 6 71 | Mut_69 84 32 57 48 72 33 58 45 82 2 72 | Mut_70 67 40 40 56 75 26 80 25 95 2 73 | Mut_71 85 20 50 26 72 26 61 31 81 10 74 | Mut_72 73 26 45 56 67 23 68 42 75 8 75 | Mut_73 102 19 95 0 103 0 86 8 111 0 76 | Mut_74 83 11 76 0 103 0 117 14 102 0 77 | Mut_75 84 10 97 0 107 0 72 9 105 0 78 | Mut_76 77 21 79 40 95 23 95 4 85 0 79 | Mut_77 89 10 64 29 89 21 98 4 97 0 80 | Mut_78 100 20 71 30 92 19 99 7 95 0 81 | Mut_79 76 12 73 28 61 23 125 3 102 0 82 | Mut_80 109 20 76 33 80 12 96 0 101 0 83 | Mut_81 83 25 57 32 77 21 95 6 106 0 84 | Mut_82 108 0 91 0 96 3 75 8 110 0 85 | Mut_83 103 0 101 0 94 1 82 15 110 0 86 | Mut_84 110 0 119 0 101 1 73 17 97 0 87 | Mut_85 105 6 112 0 76 10 105 0 103 0 88 | Mut_86 88 6 93 0 94 8 94 0 117 0 89 | Mut_87 103 6 92 0 89 6 100 0 94 0 90 | Mut_88 89 6 122 0 88 6 117 0 91 0 91 | Mut_89 88 11 96 0 96 3 117 0 99 0 92 | Mut_90 82 6 106 0 103 5 80 0 110 0 93 | Mut_91 95 2 97 0 81 4 110 0 106 0 94 | Mut_92 115 6 98 0 104 9 94 0 105 0 95 | Mut_93 97 0 102 4 85 0 106 0 83 4 96 | Mut_94 90 0 113 4 124 0 98 0 113 7 97 | Mut_95 91 0 75 8 104 0 90 0 109 10 98 | Mut_96 101 0 81 10 100 0 110 0 105 4 99 | Mut_97 110 0 91 5 105 0 105 0 117 4 100 | Mut_98 108 0 110 10 117 0 111 0 103 3 101 | Mut_99 97 0 90 8 118 0 103 0 102 1 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_3.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 106 16 73 11 110 0 88 1 102 6 3 | Mut_1 84 12 114 9 113 0 99 0 95 11 4 | Mut_2 88 13 68 13 72 0 94 1 98 9 5 | Mut_3 84 8 89 11 92 0 105 0 96 7 6 | Mut_4 99 0 79 10 93 11 95 0 91 0 7 | Mut_5 51 39 66 29 78 34 26 47 61 37 8 | Mut_6 41 49 75 27 68 25 55 42 69 38 9 | Mut_7 52 41 83 25 58 33 55 40 66 30 10 | Mut_8 53 51 73 26 77 23 31 43 43 42 11 | Mut_9 44 45 81 26 82 29 60 55 61 34 12 | Mut_10 51 51 83 36 74 40 43 38 79 41 13 | Mut_11 56 46 80 23 78 23 50 47 47 35 14 | Mut_12 49 42 82 26 63 34 74 45 67 32 15 | Mut_13 44 40 72 31 57 31 45 48 65 33 16 | Mut_14 102 5 96 1 94 0 107 16 90 0 17 | Mut_15 106 2 89 2 96 0 115 8 83 0 18 | Mut_16 113 4 92 5 85 0 94 17 88 0 19 | Mut_17 89 6 94 1 99 0 99 9 96 0 20 | Mut_18 96 1 103 2 106 0 83 7 108 0 21 | Mut_19 88 6 84 4 116 0 93 10 101 0 22 | Mut_20 94 7 91 2 114 0 87 9 84 0 23 | Mut_21 84 2 100 3 92 0 110 11 102 0 24 | Mut_22 90 6 86 0 98 0 85 5 105 0 25 | Mut_23 95 1 111 4 96 0 77 12 89 0 26 | Mut_24 99 4 97 3 89 0 74 14 105 0 27 | Mut_25 88 5 102 3 104 0 79 21 111 0 28 | Mut_26 88 21 89 16 95 9 90 11 64 31 29 | Mut_27 84 18 73 26 95 11 81 16 70 40 30 | Mut_28 69 33 72 19 94 9 102 12 54 38 31 | Mut_29 83 28 77 15 98 8 78 6 79 30 32 | Mut_30 97 21 91 25 98 17 98 8 63 42 33 | Mut_31 84 19 83 24 86 13 96 10 75 33 34 | Mut_32 93 18 88 19 100 4 82 14 63 46 35 | Mut_33 88 20 87 23 104 7 71 14 68 34 36 | Mut_34 72 24 86 21 93 6 96 6 58 35 37 | Mut_35 77 25 89 18 78 9 79 12 63 27 38 | Mut_36 75 34 101 0 102 0 78 7 106 0 39 | Mut_37 85 26 97 0 107 0 75 6 99 0 40 | Mut_38 74 24 108 0 107 0 87 10 88 0 41 | Mut_39 78 18 105 0 110 0 78 9 100 0 42 | Mut_40 80 22 89 0 100 0 92 14 100 0 43 | Mut_41 89 24 93 0 109 0 90 14 103 0 44 | Mut_42 72 18 109 0 112 0 92 16 114 0 45 | Mut_43 69 22 85 0 115 0 76 17 97 0 46 | Mut_44 80 33 91 0 101 0 86 13 98 0 47 | Mut_45 78 24 101 0 108 0 80 11 91 0 48 | Mut_46 62 23 95 0 85 0 82 18 118 0 49 | Mut_47 74 32 139 0 102 0 81 13 106 0 50 | Mut_48 66 22 92 0 96 0 83 18 102 0 51 | Mut_49 81 25 95 0 109 0 98 11 108 0 52 | Mut_50 71 20 98 0 76 0 97 9 104 0 53 | Mut_51 73 31 92 0 105 0 89 13 104 0 54 | Mut_52 94 33 98 0 95 0 97 13 89 0 55 | Mut_53 71 24 95 0 95 0 107 14 115 0 56 | Mut_54 81 6 98 0 94 0 100 0 80 17 57 | Mut_55 93 3 106 0 88 0 103 0 69 12 58 | Mut_56 95 5 112 0 88 0 105 0 89 31 59 | Mut_57 90 4 108 0 92 0 87 0 67 22 60 | Mut_58 103 2 105 0 128 0 105 0 57 29 61 | Mut_59 88 3 89 0 97 0 96 0 79 15 62 | Mut_60 93 4 111 0 102 0 107 0 74 21 63 | Mut_61 99 3 91 0 84 0 106 0 78 29 64 | Mut_62 79 4 113 0 93 0 79 0 72 17 65 | Mut_63 89 0 93 3 94 8 110 0 95 8 66 | Mut_64 97 0 98 1 89 8 96 0 83 6 67 | Mut_65 107 0 97 2 100 12 93 0 78 4 68 | Mut_66 107 0 121 2 82 17 95 0 97 6 69 | Mut_67 108 0 99 2 107 5 92 0 88 8 70 | Mut_68 105 0 102 2 87 7 100 0 115 11 71 | Mut_69 102 0 99 3 77 11 108 0 94 6 72 | Mut_70 111 0 112 3 97 5 86 0 96 9 73 | Mut_71 89 0 107 3 96 6 97 0 85 5 74 | Mut_72 123 0 102 0 83 7 64 33 98 0 75 | Mut_73 104 0 109 0 106 5 79 18 85 0 76 | Mut_74 94 0 98 0 104 3 68 31 95 0 77 | Mut_75 96 0 88 0 101 6 88 21 103 0 78 | Mut_76 117 0 89 0 90 2 82 27 98 0 79 | Mut_77 96 0 105 0 89 7 75 28 90 0 80 | Mut_78 105 0 107 0 92 5 78 18 106 0 81 | Mut_79 89 0 105 0 105 5 82 28 88 0 82 | Mut_80 87 0 84 0 92 4 68 22 96 0 83 | Mut_81 94 0 90 0 100 6 73 23 100 0 84 | Mut_82 81 0 112 0 73 7 61 20 80 0 85 | Mut_83 88 0 112 0 96 6 71 30 96 0 86 | Mut_84 109 0 100 0 95 7 74 25 95 0 87 | Mut_85 91 0 92 0 95 6 74 22 86 0 88 | Mut_86 68 20 77 28 60 28 81 13 61 40 89 | Mut_87 72 22 70 33 70 22 82 3 72 39 90 | Mut_88 63 24 85 21 66 26 78 14 66 34 91 | Mut_89 77 18 70 21 62 25 88 12 55 35 92 | Mut_90 66 16 70 28 70 29 80 10 62 32 93 | Mut_91 89 24 78 21 85 22 91 6 61 36 94 | Mut_92 70 22 85 17 73 25 91 8 67 50 95 | Mut_93 75 30 71 15 84 32 85 12 59 32 96 | Mut_94 77 23 80 25 68 17 97 14 66 28 97 | Mut_95 77 22 77 20 73 15 82 3 57 42 98 | Mut_96 81 29 75 24 99 21 84 9 52 39 99 | Mut_97 70 19 84 29 64 27 86 16 62 24 100 | Mut_98 74 18 62 33 62 18 86 15 74 34 101 | Mut_99 70 17 72 33 84 28 84 11 78 41 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_4.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 97 1 86 0 97 4 79 25 87 0 3 | Mut_1 87 0 110 0 101 4 78 14 106 0 4 | Mut_2 79 14 98 0 105 0 109 0 78 20 5 | Mut_3 81 13 95 0 96 0 94 0 72 15 6 | Mut_4 94 21 93 0 98 0 105 0 78 12 7 | Mut_5 101 16 105 0 100 0 107 0 80 15 8 | Mut_6 70 12 101 0 103 0 96 0 83 18 9 | Mut_7 65 19 99 0 100 0 94 0 94 12 10 | Mut_8 88 0 94 0 107 7 91 13 88 0 11 | Mut_9 102 0 88 0 101 5 84 16 106 0 12 | Mut_10 117 0 94 13 85 0 87 9 92 0 13 | Mut_11 89 0 89 14 94 0 96 15 99 0 14 | Mut_12 88 0 94 15 116 0 68 11 90 0 15 | Mut_13 108 0 98 19 104 0 70 12 87 0 16 | Mut_14 106 0 92 17 88 0 87 16 99 0 17 | Mut_15 90 0 90 22 87 0 91 22 92 0 18 | Mut_16 111 0 91 18 99 0 92 16 111 0 19 | Mut_17 93 0 74 12 111 0 65 10 94 0 20 | Mut_18 83 0 93 19 102 0 74 15 99 0 21 | Mut_19 85 0 81 13 108 0 87 17 86 0 22 | Mut_20 97 0 81 15 98 0 87 14 90 0 23 | Mut_21 90 0 78 18 106 0 83 15 111 0 24 | Mut_22 104 0 80 10 104 0 73 24 95 0 25 | Mut_23 107 0 83 13 103 0 74 13 92 0 26 | Mut_24 94 0 73 15 101 0 87 17 101 0 27 | Mut_25 84 0 93 16 107 0 79 15 99 0 28 | Mut_26 106 0 78 18 92 0 73 18 104 0 29 | Mut_27 96 0 98 20 111 0 83 21 101 0 30 | Mut_28 99 0 94 16 104 0 80 16 103 0 31 | Mut_29 96 0 88 16 100 0 82 11 79 0 32 | Mut_30 94 0 66 10 104 0 78 17 106 0 33 | Mut_31 101 0 101 17 91 0 93 16 100 0 34 | Mut_32 62 45 92 16 100 0 110 0 101 18 35 | Mut_33 59 30 74 27 108 0 105 0 79 16 36 | Mut_34 68 37 73 20 116 0 107 0 85 15 37 | Mut_35 64 57 70 22 103 0 105 0 86 23 38 | Mut_36 56 34 89 26 90 0 85 0 91 28 39 | Mut_37 59 43 87 20 102 0 114 0 82 16 40 | Mut_38 62 34 91 20 99 0 121 0 93 15 41 | Mut_39 71 33 88 22 95 0 105 0 84 15 42 | Mut_40 51 40 68 28 110 0 93 0 98 19 43 | Mut_41 54 28 88 15 83 0 117 0 81 9 44 | Mut_42 48 28 89 17 98 0 100 0 88 22 45 | Mut_43 63 47 79 26 95 0 88 0 76 13 46 | Mut_44 60 39 78 21 100 0 127 0 92 18 47 | Mut_45 63 53 90 21 104 0 101 0 92 19 48 | Mut_46 58 41 83 27 90 0 115 0 92 22 49 | Mut_47 67 36 76 24 115 0 94 0 68 16 50 | Mut_48 65 42 90 23 110 0 102 0 72 16 51 | Mut_49 62 35 71 14 102 0 93 0 86 12 52 | Mut_50 60 50 69 27 103 0 101 0 71 16 53 | Mut_51 56 55 70 18 112 0 108 0 83 20 54 | Mut_52 58 40 81 26 100 0 101 0 79 20 55 | Mut_53 84 36 82 24 99 0 99 0 81 19 56 | Mut_54 62 40 93 29 88 0 103 0 86 18 57 | Mut_55 55 39 82 33 107 0 103 0 86 10 58 | Mut_56 59 39 89 22 93 0 92 0 85 16 59 | Mut_57 68 38 73 19 123 0 109 0 80 19 60 | Mut_58 70 49 80 29 88 0 95 0 84 13 61 | Mut_59 50 36 64 21 103 0 96 0 79 20 62 | Mut_60 62 43 89 27 102 0 101 0 79 15 63 | Mut_61 58 38 79 25 114 0 111 0 95 14 64 | Mut_62 72 34 71 15 78 0 101 0 86 12 65 | Mut_63 59 37 75 22 115 0 112 0 65 18 66 | Mut_64 59 41 77 25 104 0 102 0 86 18 67 | Mut_65 56 49 81 23 93 0 102 0 82 15 68 | Mut_66 64 40 63 28 95 0 81 0 79 13 69 | Mut_67 50 43 66 19 115 0 96 0 100 17 70 | Mut_68 64 39 79 17 99 0 101 0 91 12 71 | Mut_69 54 40 77 25 98 0 95 0 72 18 72 | Mut_70 74 30 82 15 132 0 96 0 74 10 73 | Mut_71 63 37 89 24 81 0 96 0 85 20 74 | Mut_72 67 38 68 16 102 0 99 0 80 21 75 | Mut_73 63 51 72 24 97 0 104 0 68 27 76 | Mut_74 112 1 86 0 80 4 60 32 96 4 77 | Mut_75 101 4 104 0 101 3 76 37 97 7 78 | Mut_76 92 1 91 0 90 11 91 20 100 6 79 | Mut_77 99 1 101 0 102 4 54 28 96 11 80 | Mut_78 94 3 102 0 76 6 66 29 80 8 81 | Mut_79 103 1 87 0 95 5 73 34 98 4 82 | Mut_80 89 5 104 0 100 5 56 29 111 5 83 | Mut_81 99 1 85 0 104 6 86 27 91 9 84 | Mut_82 81 2 96 0 89 7 64 27 99 4 85 | Mut_83 59 34 65 33 82 4 53 44 67 29 86 | Mut_84 46 38 66 36 92 4 64 42 86 24 87 | Mut_85 57 44 67 46 106 2 58 41 87 21 88 | Mut_86 55 54 73 28 114 4 48 53 74 24 89 | Mut_87 61 46 54 31 103 9 53 58 69 27 90 | Mut_88 91 1 95 0 89 0 82 0 89 7 91 | Mut_89 102 2 92 0 93 0 87 0 90 2 92 | Mut_90 105 1 104 0 93 0 104 0 94 8 93 | Mut_91 105 1 107 0 120 0 99 0 97 6 94 | Mut_92 83 3 104 0 110 0 103 0 87 7 95 | Mut_93 109 3 97 0 99 0 111 0 86 5 96 | Mut_94 94 1 122 0 109 0 92 0 93 6 97 | Mut_95 84 2 109 0 100 0 93 0 89 2 98 | Mut_96 124 0 99 0 96 0 103 16 103 0 99 | Mut_97 102 0 120 0 96 0 98 12 110 0 100 | Mut_98 91 0 91 0 108 0 114 16 94 0 101 | Mut_99 114 0 72 0 111 0 88 13 108 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_5.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 47 51 65 31 42 49 66 46 51 31 3 | Mut_1 48 47 58 37 51 44 51 45 41 41 4 | Mut_2 58 60 70 23 59 45 63 46 70 43 5 | Mut_3 43 55 72 25 59 39 72 37 60 42 6 | Mut_4 52 45 67 31 61 36 66 45 46 39 7 | Mut_5 47 52 81 35 63 56 56 35 66 44 8 | Mut_6 43 55 60 37 53 43 58 40 58 41 9 | Mut_7 81 8 103 0 90 1 70 41 112 1 10 | Mut_8 96 8 101 0 99 2 70 32 97 3 11 | Mut_9 79 9 103 0 104 1 69 29 88 3 12 | Mut_10 113 8 119 0 81 0 72 36 91 3 13 | Mut_11 87 6 95 0 101 1 72 27 98 2 14 | Mut_12 77 5 119 0 105 0 76 28 99 4 15 | Mut_13 105 8 92 0 103 1 56 36 88 2 16 | Mut_14 51 58 61 21 63 42 68 26 54 51 17 | Mut_15 50 48 80 27 44 57 57 43 53 29 18 | Mut_16 54 49 68 29 60 45 55 53 65 44 19 | Mut_17 45 57 64 33 50 45 66 32 52 55 20 | Mut_18 55 45 80 43 64 42 43 44 64 29 21 | Mut_19 57 48 64 30 56 36 53 46 55 53 22 | Mut_20 100 0 68 15 78 21 105 0 115 0 23 | Mut_21 103 0 75 23 81 17 111 0 90 0 24 | Mut_22 101 0 77 34 78 27 92 0 100 0 25 | Mut_23 92 0 72 34 80 22 98 0 94 0 26 | Mut_24 107 9 98 0 102 0 81 1 48 44 27 | Mut_25 95 6 100 0 122 0 118 0 64 35 28 | Mut_26 83 6 96 0 101 0 97 0 64 29 29 | Mut_27 104 9 115 0 112 0 114 0 67 39 30 | Mut_28 88 11 95 0 77 0 98 0 62 33 31 | Mut_29 108 5 108 0 104 0 89 0 71 46 32 | Mut_30 104 11 98 0 98 0 105 0 78 38 33 | Mut_31 79 5 101 0 93 0 106 1 67 31 34 | Mut_32 103 10 106 0 107 0 115 1 75 28 35 | Mut_33 96 11 105 0 110 0 95 0 53 34 36 | Mut_34 85 9 86 0 105 0 93 0 50 34 37 | Mut_35 97 16 95 0 99 0 97 1 59 45 38 | Mut_36 77 10 88 0 117 0 94 0 67 51 39 | Mut_37 104 6 87 0 100 0 116 0 73 29 40 | Mut_38 98 1 109 0 98 0 115 0 105 0 41 | Mut_39 114 2 109 0 108 0 86 0 109 0 42 | Mut_40 103 1 109 0 99 0 106 0 100 0 43 | Mut_41 97 2 91 0 106 0 99 0 99 0 44 | Mut_42 86 1 95 0 121 0 100 0 95 0 45 | Mut_43 109 1 97 0 107 0 86 0 87 0 46 | Mut_44 108 2 96 0 96 0 112 0 85 0 47 | Mut_45 76 36 98 1 74 10 111 0 43 41 48 | Mut_46 61 30 113 4 78 30 105 1 65 39 49 | Mut_47 61 52 91 1 59 26 102 1 65 35 50 | Mut_48 66 40 106 3 82 29 103 1 57 36 51 | Mut_49 70 42 106 2 74 15 95 0 45 37 52 | Mut_50 59 39 106 0 75 21 105 1 57 51 53 | Mut_51 44 45 82 3 85 21 93 0 54 37 54 | Mut_52 65 40 111 4 79 20 87 1 50 43 55 | Mut_53 62 46 78 1 74 15 115 0 63 46 56 | Mut_54 64 40 92 1 71 28 99 0 62 31 57 | Mut_55 74 35 89 2 87 24 107 0 62 35 58 | Mut_56 55 38 102 4 76 22 98 0 60 45 59 | Mut_57 67 29 89 5 67 31 95 1 58 41 60 | Mut_58 74 34 113 0 70 20 101 0 73 49 61 | Mut_59 63 39 123 2 75 20 92 1 44 52 62 | Mut_60 58 41 100 6 90 19 95 0 49 36 63 | Mut_61 66 38 93 3 79 16 114 1 55 49 64 | Mut_62 69 43 97 3 88 19 93 0 57 45 65 | Mut_63 62 27 84 2 77 16 95 1 56 54 66 | Mut_64 53 36 104 4 69 17 113 0 49 37 67 | Mut_65 65 41 104 2 100 18 111 0 62 38 68 | Mut_66 51 43 97 3 78 22 106 0 51 46 69 | Mut_67 48 37 81 0 76 30 99 0 57 48 70 | Mut_68 51 28 98 1 79 15 92 0 58 52 71 | Mut_69 75 33 87 1 66 20 101 1 51 45 72 | Mut_70 56 42 92 2 77 24 87 0 51 37 73 | Mut_71 65 38 94 1 73 14 82 1 65 45 74 | Mut_72 80 32 102 2 70 16 92 0 58 44 75 | Mut_73 44 41 85 2 82 25 105 0 59 46 76 | Mut_74 50 34 93 2 77 29 112 0 56 38 77 | Mut_75 97 8 124 0 114 0 86 0 57 37 78 | Mut_76 92 9 86 0 100 0 107 0 52 45 79 | Mut_77 90 11 78 0 112 0 99 0 67 51 80 | Mut_78 90 8 78 0 94 0 77 0 52 45 81 | Mut_79 98 5 91 0 109 0 95 0 67 37 82 | Mut_80 92 9 80 0 115 0 94 0 65 39 83 | Mut_81 93 10 87 0 101 0 94 1 54 48 84 | Mut_82 94 7 92 0 84 0 120 2 61 39 85 | Mut_83 103 10 90 0 88 0 92 0 62 53 86 | Mut_84 94 9 82 0 114 0 129 0 53 42 87 | Mut_85 85 12 109 0 88 0 100 0 61 27 88 | Mut_86 73 6 103 0 86 0 109 0 69 43 89 | Mut_87 91 9 116 0 105 0 89 1 62 49 90 | Mut_88 106 0 87 22 78 22 122 0 107 0 91 | Mut_89 62 16 107 0 80 17 91 0 103 0 92 | Mut_90 51 41 88 0 82 23 115 0 84 2 93 | Mut_91 64 27 106 0 81 13 110 0 111 2 94 | Mut_92 70 33 104 0 75 21 109 0 86 1 95 | Mut_93 58 26 93 0 71 23 84 0 99 2 96 | Mut_94 64 30 90 0 77 21 76 0 124 1 97 | Mut_95 59 33 89 0 88 24 90 0 86 3 98 | Mut_96 56 26 113 0 87 15 104 0 105 3 99 | Mut_97 61 26 115 0 74 23 88 0 93 1 100 | Mut_98 56 31 87 0 72 25 101 0 87 1 101 | Mut_99 67 25 101 0 80 19 99 0 107 0 102 | -------------------------------------------------------------------------------- /data/simulated/Cov_100_Samples_5_Mut_100_Clone_10_PCR_Removed/sim_0.input: -------------------------------------------------------------------------------- 1 | gene_id 0 0 1 1 2 2 3 3 4 4 2 | Mut_0 93 0 103 0 98 1 98 0 72 24 3 | Mut_1 92 0 95 0 93 2 91 0 80 12 4 | Mut_2 87 0 93 0 94 3 110 0 85 24 5 | Mut_3 99 0 104 0 102 3 102 0 79 21 6 | Mut_4 91 0 100 0 97 4 99 0 70 10 7 | Mut_5 93 0 96 0 111 2 88 0 89 12 8 | Mut_6 72 0 96 0 125 4 92 0 92 19 9 | Mut_7 108 0 91 0 106 2 116 0 75 13 10 | Mut_8 110 0 93 0 71 2 93 0 81 16 11 | Mut_9 91 0 101 0 89 4 104 0 85 18 12 | Mut_10 95 0 104 0 100 2 100 0 95 11 13 | Mut_11 99 9 79 16 76 18 84 6 83 29 14 | Mut_12 70 3 72 16 98 26 87 4 77 17 15 | Mut_13 111 5 77 12 62 20 80 16 64 26 16 | Mut_14 103 7 76 17 78 31 96 10 74 22 17 | Mut_15 96 10 79 17 87 28 86 8 80 17 18 | Mut_16 85 7 81 17 82 26 110 5 82 18 19 | Mut_17 90 7 77 18 83 15 89 14 78 25 20 | Mut_18 67 5 85 14 86 24 91 5 81 25 21 | Mut_19 83 4 100 20 86 17 87 6 70 28 22 | Mut_20 105 7 81 15 76 25 107 9 76 24 23 | Mut_21 106 13 103 15 88 30 98 6 77 28 24 | Mut_22 73 5 89 10 110 0 111 0 104 0 25 | Mut_23 89 11 78 7 97 0 109 0 112 0 26 | Mut_24 109 12 99 16 90 0 102 0 94 0 27 | Mut_25 102 8 76 10 98 0 101 0 102 0 28 | Mut_26 110 4 91 11 99 0 115 0 120 0 29 | Mut_27 88 7 97 14 98 0 99 0 108 0 30 | Mut_28 86 9 72 12 99 0 108 0 109 0 31 | Mut_29 92 7 101 9 102 0 106 0 102 0 32 | Mut_30 110 9 93 10 106 0 101 0 99 0 33 | Mut_31 90 9 86 8 121 0 100 0 98 0 34 | Mut_32 85 2 104 8 105 0 84 0 99 0 35 | Mut_33 96 16 84 16 81 0 89 0 96 0 36 | Mut_34 94 6 80 13 92 0 105 0 104 0 37 | Mut_35 83 9 76 10 97 0 100 0 96 0 38 | Mut_36 88 5 82 10 112 0 108 0 117 0 39 | Mut_37 92 6 100 9 97 0 113 0 95 0 40 | Mut_38 104 9 89 14 122 0 102 0 100 0 41 | Mut_39 80 11 91 10 105 0 107 0 104 0 42 | Mut_40 82 6 88 14 100 0 96 0 104 0 43 | Mut_41 89 7 88 11 102 0 108 0 110 0 44 | Mut_42 104 9 85 11 111 0 118 0 109 0 45 | Mut_43 76 8 96 9 87 0 95 0 102 0 46 | Mut_44 92 5 91 8 86 0 108 0 106 0 47 | Mut_45 78 7 82 10 88 0 76 0 108 0 48 | Mut_46 113 8 99 15 92 0 98 0 106 0 49 | Mut_47 99 7 88 13 111 0 79 0 115 0 50 | Mut_48 74 6 91 11 101 0 98 0 121 0 51 | Mut_49 100 0 100 0 106 1 73 9 76 19 52 | Mut_50 91 0 115 0 87 2 94 12 77 21 53 | Mut_51 89 0 96 0 98 3 101 12 71 13 54 | Mut_52 124 0 113 0 95 5 85 15 67 15 55 | Mut_53 102 0 116 0 113 1 99 17 91 16 56 | Mut_54 86 0 97 0 89 8 96 16 91 12 57 | Mut_55 92 11 91 4 93 0 93 7 109 0 58 | Mut_56 94 5 99 0 90 0 93 8 104 0 59 | Mut_57 88 21 87 27 63 34 71 27 53 53 60 | Mut_58 82 17 84 13 81 31 70 44 28 42 61 | Mut_59 83 17 81 19 73 30 53 28 64 54 62 | Mut_60 71 26 79 26 76 31 72 39 45 53 63 | Mut_61 84 24 81 20 67 34 80 36 46 39 64 | Mut_62 81 17 74 19 72 36 67 34 33 49 65 | Mut_63 92 10 60 29 63 36 77 44 49 46 66 | Mut_64 70 14 78 19 69 33 54 39 41 55 67 | Mut_65 81 11 73 16 70 38 62 35 50 59 68 | Mut_66 96 10 92 25 74 32 63 31 40 42 69 | Mut_67 69 22 90 25 48 26 66 34 43 48 70 | Mut_68 81 16 78 29 58 24 64 25 60 44 71 | Mut_69 84 23 73 19 60 34 62 32 47 51 72 | Mut_70 81 15 71 23 58 25 68 35 54 50 73 | Mut_71 76 17 86 32 68 32 56 35 51 39 74 | Mut_72 75 13 73 17 63 26 61 37 53 54 75 | Mut_73 90 20 73 28 71 39 82 33 65 46 76 | Mut_74 93 16 73 14 69 42 69 33 47 55 77 | Mut_75 81 26 86 28 78 37 68 43 45 46 78 | Mut_76 85 17 78 25 80 30 57 33 57 59 79 | Mut_77 103 18 74 18 74 35 60 39 47 54 80 | Mut_78 88 14 75 19 58 35 72 38 47 47 81 | Mut_79 80 14 68 23 73 31 69 21 53 44 82 | Mut_80 84 17 74 28 67 37 56 34 55 49 83 | Mut_81 91 16 64 15 55 24 80 33 48 58 84 | Mut_82 81 21 87 23 76 40 64 34 46 42 85 | Mut_83 70 23 91 20 62 27 72 44 53 48 86 | Mut_84 81 15 76 25 73 36 70 38 49 46 87 | Mut_85 59 12 82 18 72 42 63 42 60 52 88 | Mut_86 80 24 77 27 69 45 58 37 61 43 89 | Mut_87 76 20 72 16 63 27 70 36 42 44 90 | Mut_88 87 0 95 3 118 0 96 4 104 0 91 | Mut_89 101 0 92 2 110 0 111 5 91 0 92 | Mut_90 97 0 103 3 103 0 97 5 94 0 93 | Mut_91 98 0 104 0 83 14 94 9 97 0 94 | Mut_92 100 0 78 0 84 12 83 10 101 0 95 | Mut_93 104 0 96 0 91 15 92 9 105 0 96 | Mut_94 109 0 104 0 86 14 98 6 106 0 97 | Mut_95 91 0 90 0 76 20 81 5 96 0 98 | Mut_96 92 0 83 1 110 0 110 0 76 30 99 | Mut_97 100 0 81 9 137 0 98 0 73 18 100 | Mut_98 111 0 99 4 101 0 91 0 80 27 101 | Mut_99 101 0 99 11 98 0 81 0 78 23 102 | --------------------------------------------------------------------------------