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/****************************************************************************
* *
* Loki - Programs for genetic analysis of complex traits using MCMC *
* *
* Simon Heath - University of Washington *
* *
* March 1997 *
* *
* prep.c: *
* *
* Data preperation - reading control file, reading datafiles, recoding *
* factorial data, and writing out binary datafiles for loki *
* *
* 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>
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include <string.h>
#ifdef USE_DMALLOC
#include <dmalloc.h>
#endif
#include <stdio.h>
#include <ctype.h>
#include <errno.h>
#include "version.h"
#include "ranlib.h"
#include "utils.h"
#include "libhdr.h"
#include "scan.h"
#include "control_parse.h"
#include "compat/compat.h"
#include "getopt.h"
unsigned int RunID;
int nrm_flag,strip_vars;
loki_time lt;
static int error_check=1;
static char *LogFile;
void print_version_and_exit(void)
{
(void)printf("%s\n",PREP_NAME);
exit(EXIT_SUCCESS);
}
#ifdef FUNC_NAME
#undef FUNC_NAME
#endif
#define FUNC_NAME "process_loki"
static int process_loki(int argc,char *argv[])
{
FILE *fptr;
int err,i,c,ec_flag=0;
while((c=getopt(argc,argv,"evX:d:p:"))!=-1) switch(c) {
case 'e':
error_check=0;
ec_flag=1;
break;
case 'v':
print_version_and_exit();
break; /* Previous command never returns */
case 'd':
if((i=set_file_dir(optarg))) {
fprintf(stderr,"Error setting default file directory: %s\n",i==UTL_BAD_STAT?strerror(errno):utl_error(i));
exit(EXIT_FAILURE);
}
break;
case 'p':
if((i=set_file_prefix(optarg))) {
fprintf(stderr,"Error setting default file prefix: %s\n",utl_error(i));
exit(EXIT_FAILURE);
}
break;
case 'X':
fputs("-X option must occur as first argument\n",stderr);
exit(EXIT_FAILURE);
}
if(optind>=argc) abt(__FILE__,__LINE__,"No control file specified\n");
init_stuff(&LogFile);
if((fptr=fopen(argv[optind],"r"))) err=ReadControl(fptr,argv[optind],&LogFile);
else {
(void)printf("Couldn't open '%s' for input as control file\nAborting...\n",argv[optind]);
exit(EXIT_FAILURE);
}
(void)fclose(fptr);
if(!err) {
if(getseed("seedfile",0)) init_ranf(135421);
RunID=(unsigned int)(ranf()*(double)0xffffffffU);
if(!ec_flag) error_check=syst_var[ERROR_CHECK];
print_start_time(PREP_NAME,"w",LogFile,<);
if(!scan_error_n) ReadData(LogFile); /* Read in the datafile(s) and recode (where necessary) */
}
return err;
}
#ifdef FUNC_NAME
#undef FUNC_NAME
#endif
#define FUNC_NAME "main"
int main(int argc,char *argv[])
{
int err,type=LOKI_FORMAT;
lt.start_time=time(0);
if(argc>1) {
if(*argv[1]=='-' && argv[1][1]=='X') {
type=check_format(argv[1]);
optind=2;
optreset=1;
}
}
switch(type) {
case LOKI_FORMAT:
err=process_loki(argc,argv);
break;
case QTDT_FORMAT:
err=process_qtdt(argc,argv,&LogFile,&error_check,<);
break;
default:
fputs("Input type not yet handled\n",stderr);
exit(EXIT_FAILURE);
}
if(err) {
LogFile=0;
exit(EXIT_FAILURE);
}
if(!pruned_ped_size) {
(void)printf("Zero size pedigree\nAborting...\n");
exit(EXIT_FAILURE);
}
if(!scan_error_n) {
InitFamilies(LogFile);
count_loops(LogFile);
check_inbreeding(LogFile);
check_ymark();
}
if(!scan_error_n && (traitlocus || n_markers)) err=Genotype_Elimination(syst_var[CORRECT_ERRORS],LogFile,error_check);
if(!scan_error_n && !err) nrm_flag=Calculate_NRM(LogFile);
(void)writeseed("seedfile",1);
if(family) free(family);
if(!scan_error_n && !err && nrm_flag>=0) {
WriteData(LogFile);
/* WriteXMLData(LogFile); */
WriteReport(LogFile);
}
free_nodes();
if(scan_error_n) (void)fprintf(stderr,"Errors: %d ",scan_error_n);
if(scan_warn_n) (void)fprintf(stderr,"Warnings: %d ",scan_warn_n);
if(scan_error_n || scan_warn_n) (void)fprintf(stderr,"\n");
return sig_caught;
}
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