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/****************************************************************************
* *
* Loki - Programs for genetic analysis of complex traits using MCMC *
* *
* Simon Heath - CNG, Paris *
* *
* August 2002 *
* *
* prep_utils.c: *
* *
* Copyright (C) Simon C. Heath 1997, 2000, 2002 *
* This is free software. You can distribute it and/or modify it *
* under the terms of the Modified BSD license, see the file COPYING *
* *
****************************************************************************/
#include <config.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "utils.h"
#include "libhdr.h"
#include "scan.h"
#include "control_parse.h"
#include "min_deg.h"
#include "prep_utils.h"
void print_orig_allele_id(FILE *fptr,const int i)
{
if(i>0) {
print_orig_id(fptr,i,0);
(void)fputc('m',fptr);
} else {
print_orig_id(fptr,-i,0);
(void)fputc('p',fptr);
}
}
void add_to_list(const int i,int *j,int *list)
{
int k;
for(k=0;k<(*j);k++) if(list[k]==i) break;
if(k==(*j)) list[(*j)++]=i;
}
int find_id_code(char *buf,int type,int fam)
{
struct label_data *node=0;
int i,flag;
char *p;
flag=fam<0?1:0;
if(type==INTEGER) {
i=(int)strtol(buf,&p,10);
if(*p) (void)fprintf(stderr,"Garbage after id code '%s'\n",buf);
else node=find_node(&i,type,flag);
} else node=find_node(buf,type,flag);
if(node) i=rec_tab[node->index];
else {
if(strcmp("*",buf)) {
(void)fprintf(stderr,"Id code '%s' not found\n",buf);
i=-1;
} else i=0;
}
if(fam && i>=0) i=rec_tab1[(i-1)*n_orig_families+fam-1];
else if(flag) i=-i;
return i;
}
#ifdef FUNC_NAME
#undef FUNC_NAME
#endif
#define FUNC_NAME "cat_file"
void cat_file(FILE *in,FILE *out,char *fname)
{
char buf[1024];
size_t l;
if(fseek(in,0,SEEK_SET)<0) ABT_FUNC("Couldn't seek in input file\n");
do {
l=fread(buf,1,1024,in);
if(fwrite(buf,1,l,out)!=l) DataFileError(fname);
} while(l);
}
static void blank_ind(const int i,int *blank,const int locus,const int fam)
{
int j,k;
j=ped_recode1[i-1];
if(j && blank[j-1]>=0) {
blank[j-1]=fam+1;
for(k=0;k<2;k++) id_array[i-1].haplo[k][locus]=0;
}
}
void blank_fam(const int fam,int *blank,const int locus)
{
int i,k;
i=family[fam-1].sire;
if(i) blank_ind(i,blank,locus,fam);
i=family[fam-1].dam;
if(i) blank_ind(i,blank,locus,fam);
for(k=0;k<family[fam-1].nkids;k++) {
i=family[fam-1].kids[k]+1;
blank_ind(i,blank,locus,fam);
}
}
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