From c5791f4aa4ca8915b17503e29e66b1d9031d4ce8 Mon Sep 17 00:00:00 2001 From: David Posada Date: Tue, 11 Jun 2019 16:49:54 +0200 Subject: [PATCH] examples --- examples/parameters.GTR.reads | 87 +++++++++++++++++++++++++++ examples/parameters.ISM.binary | 87 +++++++++++++++++++++++++++ examples/parameters.ISM.usergenome | 87 +++++++++++++++++++++++++++ examples/parameters.JC.usertree | 87 +++++++++++++++++++++++++++ examples/parameters.signature.noreads | 87 +++++++++++++++++++++++++++ examples/usergenome.fas | 4 ++ examples/usertree.0001 | 1 + src/cellcoal.c | 15 ++--- 8 files changed, 448 insertions(+), 7 deletions(-) create mode 100644 examples/parameters.GTR.reads create mode 100644 examples/parameters.ISM.binary create mode 100644 examples/parameters.ISM.usergenome create mode 100644 examples/parameters.JC.usertree create mode 100644 examples/parameters.signature.noreads create mode 100644 examples/usergenome.fas create mode 100644 examples/usertree.0001 diff --git a/examples/parameters.GTR.reads b/examples/parameters.GTR.reads new file mode 100644 index 0000000..d61d6e7 --- /dev/null +++ b/examples/parameters.GTR.reads @@ -0,0 +1,87 @@ +[PARAMETER FILE for CellCoal] [text in brackets will be ignored] + +[COALESCENT] + [number of replicates] n10 + [number of cells] s10 + [number of sites] l1000 + [effective population size] e10000 + [demographics] [h2 1000 100 40000 200 30000 20000] + [exponential growth rate] g1e-4 [ln2=0.6931 max] + +[GENEALOGY MODIFIERS] + [root branch length ratio] k0.1 + [outgroup branch length ratio] q0.2 + [rate variation among branches] i1 + +[MUTATION MODEL] + [alphabet binary:0 DNA:1] b1 + [germline SNP rate] [c0.00001] + [somatic mutation rate] u1e-5 + [CN_LOH rate] [H1e-5] + [deletion rate] [d1e-6] + [fixed number of mutations - ISM] [j100] + [trinucleotide genetic signature - ISM] [S1 1 1.0] [S2 11 0.3 22 0.7] + [default mutation model is ISM diploid] + [alternative mutation model ISMhap:0 Mk2:1 finiteDNA:2] m2 + [proportion of alternative model sites] p1 + [alternative/default model relative mutation rate] [w1] + [base frequencies] f0.3 0.2 0.2 0.3 + [transition/transversion ratio] [t1.7] + [rate variation among sites] [a1.0] + [mutation matrix ACGT x ACGT] [r0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] + + r0 1 2 3 + 1 0 4 5 + 2 4 0 1 + 3 5 1 0 + + [r0.00 0.03 0.12 0.04 + 0.11 0.00 0.02 0.68 + 0.68 0.02 0.00 0.11 + 0.04 0.12 0.03 0.00] + +[NGS PARAMETERS] + [genotyping error; no reads] [G0.1] + [sequencing coverage; reads simulated] C60 + [coverage overdispersion] V5 + [mat/pat allelic imbalance] [I0.5] + [ADO:allelic dropout] D0.2 + [ADO variation among sites] [P1.0] + [ADO variation among cells] [Q1.0] + [haploid coverage] [R0.5] + [amplification error] A0.5 0.01 0 + [sequencing error] E0.01 + [doublet rate per cell] [B0.0] + [error matrix ACGT x ACGT] [X0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] +[OUTPUT] + [print SNV genotypes] 1 + [print SNV haplotypes] 2 + [print full genotypes] 3 + [print full haplotypes] 4 + [print root ancestors] [5] + [print trees] 6 + [print times] [7] + [print CATG] [8] + [print true haplotypes] [9] + [print replicates in individual folders] v + [print consensus IUPAC haplotypes] [x] + [results folder name] oresults_GTR_reads + [user tree file] [Tusertree.0001] + [user genome file] [Uusergenome.fas] + +[OTHER] + [use tumor nomenclature for cells] [W] + [noisy] y1 + [seed] [#1542634305] [if no seed is specified, the current time will be used as seed] + + [noisy = 0: does not print anything + noisy = 1: + simulation summary, + noisy = 2: + replicate information, + noisy = 3: + calculation status and event information] + diff --git a/examples/parameters.ISM.binary b/examples/parameters.ISM.binary new file mode 100644 index 0000000..71802ab --- /dev/null +++ b/examples/parameters.ISM.binary @@ -0,0 +1,87 @@ +[PARAMETER FILE for CellCoal] [text in brackets will be ignored] + +[COALESCENT] + [number of replicates] n10 + [number of cells] s1000 + [number of sites] l200 + [effective population size] e10000 + [demographics] [h2 1000 100 40000 200 30000 20000] + [exponential growth rate] g1e-5 [ln2=0.6931 max] + +[GENEALOGY MODIFIERS] + [root branch length ratio] k0.1 + [outgroup branch length ratio] q0.2 + [rate variation among branches] [i1] + +[MUTATION MODEL] + [alphabet binary:0 DNA:1] b0 + [germline SNP rate] [c0.00001] + [somatic mutation rate] u1e-5 + [CN_LOH rate] [H1e-5] + [deletion rate] [d1e-6] + [fixed number of mutations - ISM] j99 + [trinucleotide genetic signature - ISM] [S1 1 1.0] [S2 11 0.3 22 0.7] + [default mutation model is ISM diploid] + [alternative mutation model ISMhap:0 Mk2:1 finiteDNA:2] [m0] + [proportion of alternative model sites] p0 + [alternative/default model relative mutation rate] [w1] + [base frequencies] [f0.3 0.2 0.2 0.3] + [transition/transversion ratio] [t1.7] + [rate variation among sites] [a1.0] + [mutation matrix ACGT x ACGT] [r0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] + + r0 1 2 3 + 1 0 4 5 + 2 4 0 1 + 3 5 1 0 + + [r0.00 0.03 0.12 0.04 + 0.11 0.00 0.02 0.68 + 0.68 0.02 0.00 0.11 + 0.04 0.12 0.03 0.00] + +[NGS PARAMETERS] + [genotyping error; no reads] G0.0 + [sequencing coverage; reads simulated] [C100] + [coverage overdispersion] [V5] + [mat/pat allelic imbalance] [I0.5] + [ADO:allelic dropout] D0 + [ADO variation among sites] [P1.0] + [ADO variation among cells] [Q1.0] + [haploid coverage] [R0.5] + [amplification error] [A0.5 0.01 0] + [sequencing error] E0.01 + [doublet rate per cell] [B0.0] + [error matrix ACGT x ACGT] [X0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] +[OUTPUT] + [print SNV genotypes] 1 + [print SNV haplotypes] 2 + [print full genotypes] 3 + [print full haplotypes] 4 + [print root ancestors] [5] + [print trees] 6 + [print times] [7] + [print CATG] [8] + [print true haplotypes] [9] + [print replicates in individual folders] v + [print consensus IUPAC haplotypes] [x] + [results folder name] oresults_ISM_binary + [user tree file] [Tusertree.0001] + [user genome file] [Uusergenome.fas] + +[OTHER] + [use tumor nomenclature for cells] [W] + [noisy] y1 + [seed] [#1542634305] [if no seed is specified, the current time will be used as seed] + + [noisy = 0: does not print anything + noisy = 1: + simulation summary, + noisy = 2: + replicate information, + noisy = 3: + calculation status and event information] + diff --git a/examples/parameters.ISM.usergenome b/examples/parameters.ISM.usergenome new file mode 100644 index 0000000..ec19466 --- /dev/null +++ b/examples/parameters.ISM.usergenome @@ -0,0 +1,87 @@ +[PARAMETER FILE for CellCoal] [text in brackets will be ignored] + +[COALESCENT] + [number of replicates] n10 + [number of cells] s40 + [number of sites] l1000 + [effective population size] e10000 + [demographics] [h2 1000 100 40000 200 30000 20000] + [exponential growth rate] g1e-5 [ln2=0.6931 max] + +[GENEALOGY MODIFIERS] + [root branch length ratio] k0.1 + [outgroup branch length ratio] q0.2 + [rate variation among branches] [i1] + +[MUTATION MODEL] + [alphabet binary:0 DNA:1] b1 + [germline SNP rate] [c0.00001] + [somatic mutation rate] u1e-6 + [CN_LOH rate] [H1e-5] + [deletion rate] d1e-7 + [fixed number of mutations - ISM] [j100] + [trinucleotide genetic signature - ISM] [S1 1 1.0] [S2 11 0.3 22 0.7] + [default mutation model is ISM diploid] + [alternative mutation model ISMhap:0 Mk2:1 finiteDNA:2] [m0] + [proportion of alternative model sites] p0 + [alternative/default model relative mutation rate] [w1] + [base frequencies] [f0.3 0.2 0.2 0.3] + [transition/transversion ratio] [t1.7] + [rate variation among sites] [a1.0] + [mutation matrix ACGT x ACGT] [r0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] + + r0 1 2 3 + 1 0 4 5 + 2 4 0 1 + 3 5 1 0 + + [r0.00 0.03 0.12 0.04 + 0.11 0.00 0.02 0.68 + 0.68 0.02 0.00 0.11 + 0.04 0.12 0.03 0.00] + +[NGS PARAMETERS] + [genotyping error; no reads] G0.0 + [sequencing coverage; reads simulated] [C100] + [coverage overdispersion] [V5] + [mat/pat allelic imbalance] [I0.5] + [ADO:allelic dropout] D0 + [ADO variation among sites] [P1.0] + [ADO variation among cells] [Q1.0] + [haploid coverage] [R0.5] + [amplification error] [A0.5 0.01 0] + [sequencing error] [E0.01] + [doublet rate per cell] [B0.0] + [error matrix ACGT x ACGT] [X0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] +[OUTPUT] + [print SNV genotypes] 1 + [print SNV haplotypes] 2 + [print full genotypes] 3 + [print full haplotypes] 4 + [print root ancestors] [5] + [print trees] 6 + [print times] [7] + [print CATG] [8] + [print true haplotypes] [9] + [print replicates in individual folders] v + [print consensus IUPAC haplotypes] [x] + [results folder name] oresults_ISM_usergenome + [user tree file] [Tusertree.0001] + [user genome file] Uusergenome.fas + +[OTHER] + [use tumor nomenclature for cells] [W] + [noisy] y1 + [seed] [#1542634305] [if no seed is specified, the current time will be used as seed] + + [noisy = 0: does not print anything + noisy = 1: + simulation summary, + noisy = 2: + replicate information, + noisy = 3: + calculation status and event information] + diff --git a/examples/parameters.JC.usertree b/examples/parameters.JC.usertree new file mode 100644 index 0000000..fae0e8c --- /dev/null +++ b/examples/parameters.JC.usertree @@ -0,0 +1,87 @@ +[PARAMETER FILE for CellCoal] [text in brackets will be ignored] + +[COALESCENT] + [number of replicates] n100 + [number of cells] s8 + [number of sites] l1000 + [effective population size] e10000 + [demographics] [h2 1000 100 40000 200 30000 20000] + [exponential growth rate] g1e-4 [ln2=0.6931 max] + +[GENEALOGY MODIFIERS] + [root branch length ratio] k0.1 + [outgroup branch length ratio] q0.2 + [rate variation among branches] [i1] + +[MUTATION MODEL] + [alphabet binary:0 DNA:1] b0 + [germline SNP rate] [c0.00001] + [somatic mutation rate] u1e-6 + [CN_LOH rate] H1e-7 + [deletion rate] [d1e-7] + [fixed number of mutations - ISM] [j100] + [trinucleotide genetic signature - ISM] [S1 1 1.0] [S2 11 0.3 22 0.7] + [default mutation model is ISM diploid] + [alternative mutation model ISMhap:0 Mk2:1 finiteDNA:2] [m0] + [proportion of alternative model sites] p1 + [alternative/default model relative mutation rate] [w1] + [base frequencies] f0.25 0.25 0.25 0.25 + [transition/transversion ratio] t0.5 + [rate variation among sites] a1.0 + [mutation matrix ACGT x ACGT] [r0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] + + [r0 1 2 3 + 1 0 4 5 + 2 4 0 1 + 3 5 1 0] + + [r0.00 0.03 0.12 0.04 + 0.11 0.00 0.02 0.68 + 0.68 0.02 0.00 0.11 + 0.04 0.12 0.03 0.00] + +[NGS PARAMETERS] + [genotyping error; no reads] G0.0 + [sequencing coverage; reads simulated] [C100] + [coverage overdispersion] [V5] + [mat/pat allelic imbalance] [I0.5] + [ADO:allelic dropout] D0 + [ADO variation among sites] [P1.0] + [ADO variation among cells] [Q1.0] + [haploid coverage] [R0.5] + [amplification error] [A0.5 0.01 0] + [sequencing error] [E0.01] + [doublet rate per cell] [B0.0] + [error matrix ACGT x ACGT] [X0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] +[OUTPUT] + [print SNV genotypes] 1 + [print SNV haplotypes] 2 + [print full genotypes] 3 + [print full haplotypes] 4 + [print root ancestors] [5] + [print trees] 6 + [print times] [7] + [print CATG] [8] + [print true haplotypes] [9] + [print replicates in individual folders] v + [print consensus IUPAC haplotypes] [x] + [results folder name] oresults_JC_usertree + [user tree file] Tusertree.0001 + [user genome file] [Uusergenome.fas] + +[OTHER] + [use tumor nomenclature for cells] [W] + [noisy] y2 + [seed] [#1542634305] [if no seed is specified, the current time will be used as seed] + + [noisy = 0: does not print anything + noisy = 1: + simulation summary, + noisy = 2: + replicate information, + noisy = 3: + calculation status and event information] + diff --git a/examples/parameters.signature.noreads b/examples/parameters.signature.noreads new file mode 100644 index 0000000..019cc40 --- /dev/null +++ b/examples/parameters.signature.noreads @@ -0,0 +1,87 @@ +[PARAMETER FILE for CellCoal] [text in brackets will be ignored] + +[COALESCENT] + [number of replicates] n10 + [number of cells] s50 + [number of sites] l10000 + [effective population size] e10000 + [demographics] [h2 1000 100 40000 200 30000 20000] + [exponential growth rate] g1e-4 [ln2=0.6931 max] + +[GENEALOGY MODIFIERS] + [root branch length ratio] k0.3 + [outgroup branch length ratio] q0.1 + [rate variation among branches] i1 + +[MUTATION MODEL] + [alphabet binary:0 DNA:1] b1 + [germline SNP rate] [c0.00001] + [somatic mutation rate] u1e-6 + [CN_LOH rate] [H1e-5] + [deletion rate] [d1e-6] + [fixed number of mutations - ISM] j100 + [trinucleotide genetic signature - ISM] S1 1 1.0 [S2 11 0.3 22 0.7] + [default mutation model is ISM diploid] + [alternative mutation model ISMhap:0 Mk2:1 finiteDNA:2] [m0] + [proportion of alternative model sites] p1 + [alternative/default model relative mutation rate] [w1] + [base frequencies] [f0.3 0.2 0.2 0.3] + [transition/transversion ratio] [t1.7] + [rate variation among sites] [a1.0] + [mutation matrix ACGT x ACGT] [r0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] + + [r0 1 2 3 + 1 0 4 5 + 2 4 0 1 + 3 5 1 0] + + [r0.00 0.03 0.12 0.04 + 0.11 0.00 0.02 0.68 + 0.68 0.02 0.00 0.11 + 0.04 0.12 0.03 0.00] + +[NGS PARAMETERS] + [genotyping error; no reads] G0.1 + [sequencing coverage; reads simulated] [C100] + [coverage overdispersion] [V5] + [mat/pat allelic imbalance] [I0.5] + [ADO:allelic dropout] D0.2 + [ADO variation among sites] [P1.0] + [ADO variation among cells] [Q1.0] + [haploid coverage] [R0.5] + [amplification error] [A0.0 0.00 0] + [sequencing error] [E0.00] + [doublet rate per cell] [B0.0] + [error matrix ACGT x ACGT] [X0 1 1 1 + 1 0 1 1 + 1 1 0 1 + 1 1 1 0] +[OUTPUT] + [print SNV genotypes] 1 + [print SNV haplotypes] 2 + [print full genotypes] 3 + [print full haplotypes] 4 + [print root ancestors] [5] + [print trees] 6 + [print times] [7] + [print CATG] [8] + [print true haplotypes] [9] + [print replicates in individual folders] v + [print consensus IUPAC haplotypes] [x] + [results folder name] oresults_signature_noreads + [user tree file] [Tusertree.0001] + [user genome file] [Uusergenome.fas] + +[OTHER] + [use tumor nomenclature for cells] [W] + [noisy] y1 + [seed] [#1542634305] [if no seed is specified, the current time will be used as seed] + + [noisy = 0: does not print anything + noisy = 1: + simulation summary, + noisy = 2: + replicate information, + noisy = 3: + calculation status and event information] + diff --git a/examples/usergenome.fas b/examples/usergenome.fas new file mode 100644 index 0000000..4026b32 --- /dev/null +++ b/examples/usergenome.fas @@ -0,0 +1,4 @@ +>maternal genome +AAAAAAACCTGAAACCTTCAGAAGCTGTTTCAGTAGGTAAAGAAAAAGGCTGGCTCTATTGAAGAAATCTGGGGGAGGTAATGCCAGATGCAGCCCAGCCGTGCGTTATAAGCTGACATGAATCAACAATAAAAAAATGCCCCCTGAAATTGGGGAAAGGTCTTCAGCATAATAACTGACTGGTTTCCATTTAACCCAGAGCACTGAGAAATCAAGGCCAATAACTTTAACGGTCAGTTTCACATGAGGGGGTGTAACTCCTCTTTCATATCCACCCATAAAAAAACACCCTCTGTATCCCAGGGAGGACTTGTTCTAGTAACTGGTGGGGACCAATGAGCTGGACAAAAAGGAATGTAAGGATTGCTCCACACCTTGCATTATGACAAGGGCATGGAATCTTACAGGAAATTTTGGGGGCTCGTACAGCAAAATTTCTAACATAGGGTTGGCCATGCATTGGGGTGTAGCCAGCCTGCATATCTCAGAAAATAACTCTCTGAAGGGACATTCATACTTAAATTTTCTTAGGTTCATGTGCTGACACGGGCCTTATACACCCTTGAACAAAAATTCAAGACAGTGTCTTCTAGATATATCAAACCTAGGGTACCCTATCTTGACTATATTACATACAAACATCTCCCCGTGTGCTGTTAAAAGAGAAAACAGCCAAATATATCTAAGCTTTTTGCTCCATTGTATCATGTATTTTATAGCAATCACTTCCTCTTTTCTCATGTTCCACCACTGAGCTCAGCTGTTCTTCATCCTGGTATGATCTACTATTCTGAATGCTGGCTCGCATTTATAACAAGAATTGCTTAGTTTTCTCAGCTATACCGTCTGGTTTAACCCTGCCTAACACTCCCTGATTCTGATGACTGGTACAAATCAGGGAGGCAAGCATTGTGGAACAACAGTTCATCCAGCAGAAACTCTCTTGTATGCTAAGGCACAGAGTTCTCTGTCAGCAGTTTCAGTTTTTTGGTCCTGTGCTCAGGATACAAAACTCTAAACCCAAAAGCTCATAAGAGTCTCTGGTACACTGTGTATATAATCTAGAGTTCAGGATACTTCCTTTTATTGCCTGTACGGTGGCTGCTTCTACAGAAAAGGGATTCAAATTCACATGATCTCACAGGGGAGCTCAGCATGCAAGCAATCTAGCAAATGGCAAACCACACACCCAATTTACTTTTAGCTTACAGGGTAGCTTATCTTTAAACATTAGCTCTTATAGGCTGATAAATCATAAACCAGACAGATCCCCCCTCATGGTGTCCCAGTTTTGGAATTAGGATGAGGGATTGTCCTTAGGGTATTTTGTAGGAGAATCCACGCATTTTGCGACAAAAACCTGAGGGGAGACCTTAAAATGAAAATCTCTTGAGTTTTAACTTTGAATACAGCAATGCCCCGGTTCAGAGATGTTCAGATGATGGGAATTCACTATCAGTGCTCACAAGCTGGATGGTCTGGTAACCTTGCCCAGAAGTTCCAGTCAGAGAAATCCACAGAAGCAGGTGCTCCTCCCCCAAGAAATCCAGGAGTCTAACATTTCCTGAAAACCCATAAGCCCTCTGTGGTGTGCATTAGAGCCTCTTTGCCACAAGGCAGGAGAGAATATAGTTGATTGTAGAGTATCTAAGCTATCTAGTAGAGTGCTCAAGAATAGTGTAAAAGTAAGCACTTAACATATGAAGATGTGGCTACAGACCAGCTCCCTAGTTCTGGACAGCACCTCGGATGGGAGTTCTCGCAACTGCATTACTCTTTCTTGAGACCTTTTGTTCTTATGTGAGGTGCAGAAATGACAACTCTCCATTTGCAAGATGACAAGCTTAAACTATACCTTTCTAAGAAAACATCTGACCAAATACAGAAACTGTGTGTTGGCTCTCTCGACTCTGCATAAAGTATCCTTAGGTTATCAGAACCCCCCCTCAGTCCAGAAAATGTCCAGTGAGCCCAAGACAGCTTATTAGAGAGAAGAGATTTTTTACAACAAAGACACAGAAGGGAATCATTTTACCTGGCTCCCCCCTAGGACAAAGTTTTGGGTATATTTCCTTTTAAAAAGGGCTCAATATGGACCCTTTAGAAGACACAAGGCAACTGCCATGTTTTTGCTGAAAGACTAGATTTTTTAACCAGACCGAACAAAATGCTTATGTGGCTCTTGTTGAATAGCAGACATTGCCTGACATAAAGAAACCAACAGGCAAAAAAATGAGTGTTGTTGTAAATTTCCACTGCTGCTCCCAATGTGCCTTTGGGAGCTGTGGAATTTCAACAGTTGCCAGAGCCTGACGACCAAGCTGACGCTGAGATGGCACAGATTAGATTCATGAGGCTGAGATGAGGAGAGTCAAGTTTGGTGTGAGAACAAACTTATTCCAGTCCTTAAGCGCCTTTGACGATCAAAGATAGCATGAGGGTGGACGAGAAGTGTATTGTCTGATATATTGCCTCCCACGCAAAAAAACCTGAGTTCTTTTTATTAAACCTTTATAAATGAAGATCATCTCAGTAGTTGTTATGTGATTTTCTCCAACGTTTTAATCCCTAAAAAAGATTGGCAGAACATGAGACTGATCCTGACTCAGAAAGGGAAGACAGTTTTCCTGGACTGTGGGCAAGAATGTATATTGTTGGTATTCCTTTTGATATAAGTGGTCCCCCATTGATATAATTTTCTTTCATATCAGGGTGGAAAGCGTTGATTACAGCCGACAAAAATGCCATTAAAGGTTCACCCTTGGCTTATTGTGGTCTTTGTCAAAATACATTATAGATGCTGTTTTAGGAGTGTCAAAAAGGGAGAACCTATAAGCTAAGCCGATACTCCATATGCTCATTAATGGGGAAACGTGCTATAATAAAGCAGGAAATGGGCGCTGATTCTAAAATACGTGTGTGCTTCTACCTTCATTGCAATGGGCACATAGATCTAAGGGGATTTTTATTAGGTTTAACATACAGAAAGAGAGGGCCGGCAGGACAAATGTTGCTGCCAAGGTCCAAGAAACGTACTTATTGATGTTAAACAGCATGGTATAATAGAGAGGATGCTAATCACAATAAGGAGGGAAATTTTCTGTTTTGTGAGGCATTCACCTTCACTTTCGAGAAATCAGGCTCTCATTGGAAGTCTTACATTTTGCAGAAAAAGGAAAGTCAGTTTAGATTTAACAGCTTTAGGCTTAAAATCCCCTTTATGTATCTTGCGAAAGTATTACAGTAGCTGTGCTCTATCACAGGTGCTATGAGTTTCAAGCAGATAAATAATTGCATATGAGCCAGCACACTGGCATTTATAAAAAAAATGCTAAAGTATCGTAAGAGGGCATGCAGCCATAAGTGGTCTTATTTCCAGGTGGGGGGAGGCATCCATAGGGAACAGAATTTTTGAAAGGAGGTAGAGGCCCCTGAGAGTGAGTAATGTTCTATTCATCTGTTACCTTTTTAGGAACCCCAAGGGCACACTTCTCTCTTGGATCTTACTCAACTGTCCTCAAATACAGAGAGCTGCCAAAGAAAACAGGGAGAGTAACACACTCCTCTGACCAACAGAGGAGGAGGCACATCAGCCTAGAAGTCCCAGATGCATAAAACAGATGATGATGTTGTCCACAATCTCTGTCATCATTTGAATATTTCTACATGTGATGAGATGGGGCCTGTGAGGGTGAGATCACCAGT +>paternal genome +AAAAAAACCTGAAACCTTCAGAAGCTGTTTCAGTAGGTAAAGAAAAAGGCTGGCTCTATTGAAGAAATCTGGGGGAGGTAATGCCAGATGCAGCCCAGCCGTGCGTTATAAGCTGACATGAATCAACAATAAAAAAATGCCCCCTGAAATTGGGGAAAGGTCTTCAGCATAATAACTGACTGGTTTCCATTTAACCCAGAGCACTGAGAAATCAAGGCCAATAACTTTAACGGTCAGTTTCACATGAGGGGGTGTAACTCCTCTTTCATATCCACCCATAAAAAAACACCCTCTGTATCCCAGGGAGGACTTGTTCTAGTAACTGGTGGGGACCAATGAGCTGGACAAAAAGGAATGTAAGGATTGCTCCACACCTTGCATTATGACAAGGGCATGGAATCTTACAGGAAATTTTGGGGGCTCGTACAGCAAAATTTCTAACATAGGGTTGGCCATGCATTGGGGTGTAGCCAGCCTGCATATCTCAGAAAATAACTCTCTGAAGGGACATTCATACTTAAATTTTCTTAGGTTCATGTGCTGACACGGGCCTTATACACCCTTGAACAAAAATTCAAGACAGTGTCTTCTAGATATATCAAACCTAGGGTACCCTATCTTGACTATATTACATACAAACATCTCCCCGTGTGCTGTTAAAAGAGAAAACAGCCAAATATATCTAAGCTTTTTGCTCCATTGTATCATGTATTTTATAGCAATCACTTCCTCTTTTCTCATGTTCCACCACTGAGCTCAGCTGTTCTTCATCCTGGTATGATCTACTATTCTGAATGCTGGCTCGCATTTATAACAAGAATTGCTTAGTTTTCTCAGCTATACCGTCTGGTTTAACCCTGCCTAACACTCCCTGATTCTGATGACTGGTACAAATCAGGGAGGCAAGCATTGTGGAACAACAGTTCATCCAGCAGAAACTCTCTTGTATGCTAAGGCACAGAGTTCTCTGTCAGCAGTTTCAGTTTTTTGGTCCTGTGCTCAGGATACAAAACTCTAAACCCAAAAGCTCATAAGAGTCTCTGGTACACTGTGTATATAATCTAGAGTTCAGGATACTTCCTTTTATTGCCTGTACGGTGGCTGCTTCTACAGAAAAGGGATTCAAATTCACATGATCTCACAGGGGAGCTCAGCATGCAAGCAATCTAGCAAATGGCAAACCACACACCCAATTTACTTTTAGCTTACAGGGTAGCTTATCTTTAAACATTAGCTCTTATAGGCTGATAAATCATAAACCAGACAGATCCCCCCTCATGGTGTCCCAGTTTTGGAATTAGGATGAGGGATTGTCCTTAGGGTATTTTGTAGGAGAATCCACGCATTTTGCGACAAAAACCTGAGGGGAGACCTTAAAATGAAAATCTCTTGAGTTTTAACTTTGAATACAGCAATGCCCCGGTTCAGAGATGTTCAGATGATGGGAATTCACTATCAGTGCTCACAAGCTGGATGGTCTGGTAACCTTGCCCAGAAGTTCCAGTCAGAGAAATCCACAGAAGCAGGTGCTCCTCCCCCAAGAAATCCAGGAGTCTAACATTTCCTGAAAACCCATAAGCCCTCTGTGGTGTGCATTAGAGCCTCTTTGCCACAAGGCAGGAGAGAATATAGTTGATTGTAGAGTATCTAAGCTATCTAGTAGAGTGCTCAAGAATAGTGTAAAAGTAAGCACTTAACATATGAAGATGTGGCTACAGACCAGCTCCCTAGTTCTGGACAGCACCTCGGATGGGAGTTCTCGCAACTGCATTACTCTTTCTTGAGACCTTTTGTTCTTATGTGAGGTGCAGAAATGACAACTCTCCATTTGCAAGATGACAAGCTTAAACTATACCTTTCTAAGAAAACATCTGACCAAATACAGAAACTGTGTGTTGGCTCTCTCGACTCTGCATAAAGTATCCTTAGGTTATCAGAACCCCCCCTCAGTCCAGAAAATGTCCAGTGAGCCCAAGACAGCTTATTAGAGAGAAGAGATTTTTTACAACAAAGACACAGAAGGGAATCATTTTACCTGGCTCCCCCCTAGGACAAAGTTTTGGGTATATTTCCTTTTAAAAAGGGCTCAATATGGACCCTTTAGAAGACACAAGGCAACTGCCATGTTTTTGCTGAAAGACTAGATTTTTTAACCAGACCGAACAAAATGCTTATGTGGCTCTTGTTGAATAGCAGACATTGCCTGACATAAAGAAACCAACAGGCAAAAAAATGAGTGTTGTTGTAAATTTCCACTGCTGCTCCCAATGTGCCTTTGGGAGCTGTGGAATTTCAACAGTTGCCAGAGCCTGACGACCAAGCTGACGCTGAGATGGCACAGATTAGATTCATGAGGCTGAGATGAGGAGAGTCAAGTTTGGTGTGAGAACAAACTTATTCCAGTCCTTAAGCGCCTTTGACGATCAAAGATAGCATGAGGGTGGACGAGAAGTGTATTGTCTGATATATTGCCTCCCACGCAAAAAAACCTGAGTTCTTTTTATTAAACCTTTATAAATGAAGATCATCTCAGTAGTTGTTATGTGATTTTCTCCAACGTTTTAATCCCTAAAAAAGATTGGCAGAACATGAGACTGATCCTGACTCAGAAAGGGAAGACAGTTTTCCTGGACTGTGGGCAAGAATGTATATTGTTGGTATTCCTTTTGATATAAGTGGTCCCCCATTGATATAATTTTCTTTCATATCAGGGTGGAAAGCGTTGATTACAGCCGACAAAAATGCCATTAAAGGTTCACCCTTGGCTTATTGTGGTCTTTGTCAAAATACATTATAGATGCTGTTTTAGGAGTGTCAAAAAGGGAGAACCTATAAGCTAAGCCGATACTCCATATGCTCATTAATGGGGAAACGTGCTATAATAAAGCAGGAAATGGGCGCTGATTCTAAAATACGTGTGTGCTTCTACCTTCATTGCAATGGGCACATAGATCTAAGGGGATTTTTATTAGGTTTAACATACAGAAAGAGAGGGCCGGCAGGACAAATGTTGCTGCCAAGGTCCAAGAAACGTACTTATTGATGTTAAACAGCATGGTATAATAGAGAGGATGCTAATCACAATAAGGAGGGAAATTTTCTGTTTTGTGAGGCATTCACCTTCACTTTCGAGAAATCAGGCTCTCATTGGAAGTCTTACATTTTGCAGAAAAAGGAAAGTCAGTTTAGATTTAACAGCTTTAGGCTTAAAATCCCCTTTATGTATCTTGCGAAAGTATTACAGTAGCTGTGCTCTATCACAGGTGCTATGAGTTTCAAGCAGATAAATAATTGCATATGAGCCAGCACACTGGCATTTATAAAAAAAATGCTAAAGTATCGTAAGAGGGCATGCAGCCATAAGTGGTCTTATTTCCAGGTGGGGGGAGGCATCCATAGGGAACAGAATTTTTGAAAGGAGGTAGAGGCCCCTGAGAGTGAGTAATGTTCTATTCATCTGTTACCTTTTTAGGAACCCCAAGGGCACACTTCTCTCTTGGATCTTACTCAACTGTCCTCAAATACAGAGAGCTGCCAAAGAAAACAGGGAGAGTAACACACTCCTCTGACCAACAGAGGAGGAGGCACATCAGCCTAGAAGTCCCAGATGCATAAAACAGATGATGATGTTGTCCACAATCTCTGTCATCATTTGAATATTTCTACATGTGATGAGATGGGGCCTGTGAGGGTGAGATCACCAGT diff --git a/examples/usertree.0001 b/examples/usertree.0001 new file mode 100644 index 0000000..e523c49 --- /dev/null +++ b/examples/usertree.0001 @@ -0,0 +1 @@ +((D:0.03,B:0.04):0.02,(C:0.06,A:0.07):0.05); diff --git a/src/cellcoal.c b/src/cellcoal.c index 6096c94..f6fce6f 100644 --- a/src/cellcoal.c +++ b/src/cellcoal.c @@ -408,7 +408,7 @@ int main (int argc, char **argv) for (dataSetNum=0; dataSetNum 0) /* we only print replicates with variation */ @@ -6718,7 +6719,7 @@ static void PrintRunInformation (FILE *fp) fprintf (fp, "\n CN-LOH rate = %2.1e", CNLOHrate); fprintf (fp, "\n Mean number of CN-LOH events = %3.2f", meanNumCNLOH); if (numDataSets > 1) - fprintf (fp, "\n Variance number of CN-LOH events = %3.2f", varNumCNLOH); + fprintf (fp, "\n Variance number of CN-LOH events = %3.2f", varNumCNLOH); } if (genotypingError > 0 || doNGS == YES) @@ -6791,8 +6792,8 @@ static void PrintCommandLine (FILE *fp, int argc,char **argv) fprintf (fp, "Command line arguments (some might not affect) = %s", CommandLine); else { - fprintf (fp, "Parameter file arguments (some might not affect) = "); - + fprintf (fp, "Parameter file [\"%s\"] arguments (some might not affect) = ", parameterFile); + /* Coalescent */ fprintf (fp, " -n%d -s%d -l%d -e%d -g%2.1e -h%d", numDataSets, numCells, numSites, N, growthRate, numPeriods); for (i=1; i<=numPeriods; i++) @@ -7656,7 +7657,7 @@ static void ReadParametersFromCommandLine (int argc,char **argv) if (alphabet == BINARY) { - fprintf (stderr, "\n!!! PARAMETER ERROR: Trinucleotide signatures cannot be simulated with the the binary alphabet"); + fprintf (stderr, "\n!!! PARAMETER ERROR: Trinucleotide signatures cannot be simulated with the binary alphabet"); PrintUsage(stderr); } @@ -8296,7 +8297,7 @@ void ReadParametersFromFile () if (alphabet == BINARY) { - fprintf (stderr, "\n!!! PARAMETER ERROR: Trinucleotide signatures cannot be simulated with the the binary alphabet"); + fprintf (stderr, "\n!!! PARAMETER ERROR: Trinucleotide signatures cannot be simulated with the binary alphabet"); PrintUsage(stderr); }