https://github.com/jsollari/popABC
Tip revision: 3ebe7b76043299bc4b6a541b5be0d7012895ca1c authored by Joao Sollari Lopes on 21 November 2017, 15:04:40 UTC
remove binaries folder
remove binaries folder
Tip revision: 3ebe7b7
interface.h
/*
@author: joao lopes
@workplace: Reading University
@date: 12th May 2009
*/
#ifndef INTERFACE_H_
#define INTERFACE_H_
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <time.h>
#include "mylib.h"
#define MAXSSTATS 15 //number of possible used summary statistics
#define MAXSSTATS_M 6 //number of possible used summary statistics for Microssatelites
#define MAXSSTATS_S 9 //number of possible used summary statistics for Sequence Data
#define COALEVNT 3 //different types of events in the Genetic Trees
#define MAXDATA 250000000 //maximum number of data (nparam+nstats)*nsim to be analysed
#define NPOP 2
#define LOCMAXCHAR 10
#define MAXMODEL 5
#define NPLOIDY 2
#define MAXCHAR 256 //max number of char of the pops names
#define MAXNPRIOR 10000 //maximum number of parameter values to be stored
// struct used to save the parameters of a prior distribution
struct prior{
int type; //Distribution of the prior
double *p; //parameters of the distribution
};
// struct used to save the migration weights matrix
struct migweights{
int type; //Distribution of the prior
double ***m; //migweights per npop per ntev per npop
};
// struct used to save the information about a gene tree
struct data{
int npop; //number of populations
int nloc; //number of loci
int **nsamp; //pointer to a 2d-array(population, number of samples)
int *tsamp; //total number of samples per loci
int ***freq; //frequency of the diferent haplotypes by loci by pop
int *ldna; //array that gives the number of all the diferent haplotypes by loci
int *Nmax; //maximum number of different alleles/haplotypes
//only used in microssatelites analysis
int **valM; //all the diferent haplotypes by loci
//only used in dna sequence analysis
int *lsites; //array(number of sites of the dna sequency (number of mutations), loci)
char ***valS; //2d-array(all the diferent haplotypes, loci)
};
// struct used to save the parameters to build a gene tree
struct params{
int npop; //number of populations
int niter; //number of iterations
int nevt; //number of events
int nrSTR; //number of linked STR's loci
double gent; //number of generation time
int ntop; //number of possible topologies
double *ploidy; //heriditage scalar per locus
char *type; //DNA type
int nloc; //number of loci
int **nsamp; //pointer to 2d array: population vs number of samples
double *mu; //pointer to array with mutation rate in diferente loci
double *rec; //pointer to array with recombination rate in different loci
int topol; //topology
int *seq; //pointer to array with information about split population events
double *tev; //pointer to array with events' times
double **psize; //2d array: populations' Ne size vs number of events + 1
double **mig; //2d array: migration rates vs number of events
};
/*
Start of the ABC program. Simulates coordenated points (summary_statistics, parameters) to be
used in an Aproximate Bayesian Computation model to estimate the true values of a genealogical tree
(sequence data).
@param input_prs - .prs input filename
@param input_ssz - .ssz input filename
@param input_sst - .sst input filename
@param output - .dat output filename
@param printIt - print or not the .len and .frq files of every genetic tree (0-don't print; 1-print)
@param printMut - print or not the .mut (0-don't print; 1-print)
@param printRec - print or not the .rec (0-don't print; 1-print)
*/
int abc(char *input_prs,char *input_ssz,char *input_sst, char* output,int printIt,int printMut,int printRec);
/*
This function samples values from the priors and stores them
Defined in samplePriors.c
@param pm - pointer to the parameters to be used in the simulation
@param outline1 - place to store all the first part of the data
@param out_mut - pointer to output file .mut
@param printMut - indicate if the mutation rates are going to be printed or not
@param foundSTR - check if STR's are present in the study
@param foundSNP - check if SNP's are present in the study
@param ltype - DNA type per loci
*/
int sampPriors(struct params *pm,char *outline1,FILE *out_mut,FILE *out_rec,int printMut,int printRec,int foundSTR,int foundSNP,char *ltype);
/*
This function calulates the summary statistics from simulated data and stores them
Defined in summStats.c
@param data - struture with the informations about a genealogical tree
@param lsstats - list of the used sstats (0-absent;1-present)
@param outp - string that will store the summary statistics
@param foundSTR - check if STR's are present in the study
@param foundSNP - check if SNP's are present in the study
@param ltype - DNA type per loci
*/
void summStats(struct data *data,int *lsstats,char *outp,int foundSTR,int foundSNP, char*ltype);
/*
This function simulats the genetic data
Defined in geneticTree.c
@param pm - parameters used to build a geneology tree
@param data - data from a geneology tree
@param printit - use to print or not the informations to a separate file
@param citer - current iteration
@param path - path where the output files are going to be store in
*/
int sampLikelihood(struct params *pm, struct data *data,int printit,long citer, char *path);
/*
Frees the memory allocated in the first iteration
Defined in abc.c
@param nloc number of loci
@param npop number of populations
@param nevt number of events
*/
void freetree(int nloc,int npop,int nevt);
/*
This function gets an sample file (.pop) and creates a table file (.len)
@param input - input filename
@param output - output filename
*/
int createFreqTab(char *intput,char *output);
/*
This function gets an IMa input file and creates a table file (.len)
@param input - input filename
@param output - output filename
*/
int createFreqTab2(char *intput,char *output);
/*
This function gets a GenePop input file and creates a table file (.len)
@param input - input filename
@param output - output filename
*/
int createFreqTab3(char *intput,char *output);
/*
This function gets a Nexus file (.nex) and creates a table file (.len)
@param input - input filename
@param output - output filename
*/
int createFreqTab4(char *intput,char *output);
/*
This funtion uses a freq_tab_length file and creates a output file which contains
the summary statistics of the given file and its sample sizes
@param input filename (*.len)
@param input filename (*.sst)
@param output filename (*.trg AND *.szz)
@return an integer to check for errors
*/
int maketarget(char *input_len,char *input_sst,char *output);
/*
This program prints out a proportion, specified by tolerance, of the simulated data with an ABC approach
which are closer in Euclidian distance to the target summary statistics. It will also create a file
which will contain the simulated populational tree parameters (only) in the first 10000 lines of the data.
These can then be used to build a posterior distributions with which we can compare prior distributions
@arg filename with simulated data
@arg filename with target summary statistics (summary statistics from our "real" data)
@arg filename of the output of the program
@arg number of parameters
@arg number of summstats
@arg tolerance of analysis (between 0 and 1)
*/
int firstpass(char *input,char *target,char *output,int nparam,int nsstas,double tol);
/*
This file creates a .prs file.
@param outname - name of the output file
@param niter - number of simulations to run
@param genet - generation time of the populations species
@param npop - number of population
@param nloc - number of loci
@param lplo - herederiter scalar per locus
@param ltype - type of DNA data per locus
@param pr_top - prior struct - topology
@param pr_Ne - list of prior struct (size=npop*2-1) - pop size
@param pr_tev - list of prior struct (size=npop-1) - tev
@param pr_mig - list of prior struct (size=2*npop-2) - mig
@param pr_mut - prior struct - mutSTR
@param pr_mut - prior struct - mutSNP
@param pr_rec - prior struct - recSTR
@param pr_rec - prior struct - recSNP
*/
int makeprior(char *output,
int niter,int genet,int npop,int nloc, //1sr line
double *lplo, //2nd line
char *ltype, //3th line
struct prior pr_top, //4th line
struct prior *pr_Ne, //5th line
struct prior *pr_tev, //6th line
struct prior *pr_mig, //7th line
struct prior pr_mutSTR, //8th line
struct prior pr_mutSNP, //9th line
struct prior pr_recSTR, //10th line
struct prior pr_recSNP, //11th line
struct migweights migw); //12th line
/*
This file creates a .sst file.
@param outname - name of the output file
@param lsstats - list of the used sstats (0 - don't use; 1 - use)
*/
int makestats(char *output,int *lsstats);
/*
This funtion takes a .len file and creates a sample populations for it
@param filename of .len file
@param filename of the output of the function
@return an integer to check for errors
*/
int makepop(char *input, char *output);
/*
It creates an ABC .len file given an IM input file.
@param input filename
@param output filename
@return a integer to check for errors
*/
int convertToABC(char *input,char *output);
/*
This function joins files together
@param ninp number of files to join
@param linp list of the input filenames to join
@param out output filename
@return an integer to check for errors
*/
int joindata(int ninp, char *linp[],char *outp);
static const int RecIter = 50000, //stepsize of iteration when the program records information
RecLine = 500000, //record step per lines analysed
DnaSizeM = 100, //size of microssatellite dna
DnaSizeS = 10; //size of dna sequence
int Exepathsize; //size of the path to the executable
char *Exepath; //path to the executable
struct prior P_top, //prior of topology
P_mutM, //hiperprior of mutation rate Microsatelites
P_mutS, //hiperprior of mutation rate Sequence data
P_recM, //hiperprior of recombination rate Microsatelites
P_recS, //hiperprior of recombination rate Sequence data
*P_t, //priors of time events
**P_mig, //prior of migration
**P_psize; //priors of Ne by events
struct migweights M_migw; //migration weights matrix
#endif /*INTERFACE_H_*/