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GetSubGeno.cpp
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GetSubGeno.cpp
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// in input it receives a file .txt lines / sites to be kept (1 based)
// in output it generates a new .geno file (binary) with only the sites retained
#include <cstdio>
#include <cstdlib>
#include <sys/stat.h>
#include <cstring>
#include <vector>
#include <math.h>
#include <string> //for str operations
using namespace std;
// a general matrix style structure
template <typename T>
struct matrix{
int x;
int y;
T** data;
};
template <typename T>
struct array{
int x;
T* data;
};
template <typename T>
T *collapse(std::vector<T> &v){
T *tmp = new T[v.size()];
for(int i=0;i<v.size();i++)
tmp[i] = v[i];
return tmp;
}
//function to cleanup our generic matrix structure
template <typename T>
void cleanup(matrix<T> &m){//using a reference to avoid copying the data
for(int i=0;i<m.x;i++)
delete [] m.data[i];
delete [] m.data;
}
// get the filesize of a file
size_t fsize(const char* fname){
struct stat st ;
stat(fname,&st);
return st.st_size;
}
// find out if a file exists
int fexists(const char* str) {
struct stat buffer ;
return (stat(str, &buffer )==0 );
}
// a nice wrapper for getting files
FILE *getFILE(const char*fname,const char* mode) {
int writeFile = 0;
for(size_t i=0;i<strlen(mode);i++)
if(mode[i]=='w')
writeFile = 1;
if(writeFile&&fexists(fname)){//DRAGON
fprintf(stderr,"\t-> File exists: %s exiting...\n",fname);
exit(0);
}
FILE *fp;
if(NULL==(fp=fopen(fname,mode))){
fprintf(stderr,"\t->Error opening FILE handle for file:%s exiting\n",fname);
exit(0);
}
return fp;
}
array<int> readArray(const char *fname, int len) {
FILE *fp = getFILE(fname,"r");
size_t filesize =fsize(fname);
if(filesize==0){
fprintf(stderr,"file:%s looks empty\n",fname);
exit(0);
}
array<int> ret;
int *tmp = new int[len];
char *buf = new char[filesize];
fread(buf,sizeof(char),filesize,fp);
tmp[0] = atoi(strtok(buf,"\t \n"));
for(int i=1;i<(len);i++)
tmp[i] = atoi(strtok(NULL,"\t \n"));
fclose(fp);
ret.x = len;
ret.data = tmp;
return ret;
}
// read a file into a matrix
matrix<double> readFile(char *fname, int nInd, int nSites) {
FILE *fp = getFILE(fname,"rb");
size_t filesize =fsize(fname);
if((filesize %(sizeof(double)*nInd*3*nSites)) ) {
fprintf(stderr,"\n\t-> Possible error,binaryfiles might be broken\n");
exit(-1);
}
double **data = new double*[nSites*nInd];
fseek(fp, 0, SEEK_SET);
for(int i=0; i<(nSites*nInd); i++) {
double *tmp = new double[3];
fread(tmp,sizeof(double),3,fp);
data[i]= tmp;
}
fclose(fp);
matrix<double> ret;
ret.x = nSites*nInd;
ret.y = 3;
ret.data = data;
return ret;
}
int main (int argc, char *argv[]) {
char *infile=NULL;
char *posfile=NULL;
char *outfile=NULL;
int argPos = 1, nind = 0, nsites = 0, increment=0, verbose=0, len=0;
// CHECK HERE FOR USAGE:
while (argPos<argc) {
increment = 0;
if(strcmp(argv[argPos],"-infile")==0)
infile = argv[argPos+1];
else if(strcmp(argv[argPos],"-posfile")==0)
posfile = argv[argPos+1];
else if(strcmp(argv[argPos],"-nind")==0)
nind = atoi(argv[argPos+1]);
else if(strcmp(argv[argPos],"-nsites")==0)
nsites = atoi(argv[argPos+1]);
else if(strcmp(argv[argPos],"-len")==0)
len = atoi(argv[argPos+1]);
else if(strcmp(argv[argPos],"-outfile")==0)
outfile = argv[argPos+1];
else if(strcmp(argv[argPos],"-verbose")==0)
verbose = atoi(argv[argPos+1]);
else {
printf("\tUnknown arguments: %s\n",argv[argPos]);
return 0;
}
argPos = argPos + 2 + increment;
}
matrix<double> geno;
geno = readFile(infile, nind, nsites);
if (verbose) fprintf(stderr, "Dim input %d , %d; example %f %f %f\n", geno.x, geno.y, geno.data[0][0], geno.data[0][1], geno.data[0][2]);
// posfile is a file newline-separated with numbers of lines/sites to keep
array<int> pos;
pos = readArray(posfile, len);
if (verbose) fprintf(stderr, "Dim pos %d; example %d %d\n", pos.x, pos.data[0], pos.data[1]);
// print
// pos is 1 based
FILE *fp = fopen(outfile,"wb");
for (int s=0; s<pos.x; s++) {
if(pos.data[s] < 1 || pos.data[s] > nsites){
fprintf(stderr, "\n\tERROR: invalid specified positions!\n");
exit(-1);
}
int row = pos.data[s]-1;
for (int i=row*nind; i<(row+1)*nind; i++)
fwrite(geno.data[i], sizeof(double), geno.y, fp);
}
fclose(fp);
} // main