int main()
{
int i;
int sum=0;
char arglist[100][256];
char* buf=NULL;
// signal(SIGTTIN,SIG_IGN); //忽略终端STOP信号
// signal(SIGTTOU,SIG_IGN);
// signal(SIGTSTP,SIG_IGN);
// signal(SIGHUP,SIG_IGN);
buf=(char*)malloc(sizeof(char)*256);
while(1)
{
memset(buf,0,256);
print_shell();
input_command(buf);
if(strcmp(buf,"exit")==0||strcmp(buf,"logout")==0)
break;
for(i=0;i<100;i++)
arglist[i][0]='\0';
sum=0;
explain_command(buf,&sum,arglist);
do_command(sum,arglist);
}
if(buf!=NULL)
free(buf);
exit(0);
}
static SRM_binning option_assign(int argc, char **argv)
{ SRM_binning args;
int c,option_index;
static struct option long_options[] =
{ {"multiplicity", required_argument ,0,0},
{"binOut",required_argument,0,2},
{"inb",required_argument,0,3},
{"perm",no_argument,0,4},
{0,0,0,0}
};
char *insert=NULL;
args.multple = 2.0;
args.quantile = 0.95;
args.bin_size = 100;
args.win_size = 200;
args.output_file = NULL;
args.binout_file = NULL;
args.inbin_file = NULL;
args.outlier_file=NULL;
args.autoselect_lambda = 0;
args.FP = 1;
args.B = 10;
args.fdr = 0;
args.lambda = 2;
args.paired = 0;
args.tumor_file = NULL;
args.normal_file = NULL;
args.insert = 220;
args.sd = 20;
args.tumor_freq = 0.5;
args.resampling = 1;
args.in_tmor = NULL;
args.in_nml = NULL;
args.output = NULL;
args.inbin = NULL;
args.outbin = NULL;
args.outlier = NULL;
while((c=getopt_long(argc,argv,"2q:b:w:o:R:hf:p:B:l:",long_options,&option_index))!=-1){
switch(c){
case 0:
args.multple = atoi(optarg);
if(args.multple<1.0) { fprintf(stderr,"Error,multiplicity must be larger than or equal to 1.0\n"); exit(1);}
break;
case 2:
args.binout_file = strdup(optarg);
break;
case 3:
args.inbin_file = strdup(optarg);
break;
case 4: args.resampling = 0;
break;
case 'l':
args.lambda = atof(optarg);
if(args.lambda<=0.0) { fprintf(stderr,"Parameter misspecification: Lambda must be positive number.\n"); exit(1);}
break;
case 'f':
args.FP = atof(optarg);
args.autoselect_lambda = 1;
if(args.FP<=0.0) {fprintf(stderr,"Expected number of type I error must be postive\n");exit(1);}
break;
case 'I':
insert = strdup(optarg);
args.paired = 1;
break;
case 'q':
args.quantile = atof(optarg);
if(args.quantile<=0.0 || args.quantile>1.0) { fprintf(stderr,"Quantile should be between 0 and 1.\n"); exit(1);}
break;
case 'b':
args.bin_size = atoi(optarg);
if(args.bin_size<1) {fprintf(stderr,"Bin size should be at least 1.\n");exit(1);}
break;
case 'w':
args.win_size = atoi(optarg);
if(args.win_size<1) {fprintf(stderr,"The window size must be positive.\n");exit(1);}
break;
case '2':
args.paired = 1;
break;
case 'o':
args.output_file = strdup(optarg);
break;
case 'R':
args.outlier_file = strdup(optarg);
case 'p':
args.tumor_freq = atof(optarg);
if(args.tumor_freq<0.0||args.tumor_freq>=1.0){fprintf(stderr,"The probabilty of a read being a tumor read must be between 0 and 1\n");exit(1);}
args.fdr = 1;
break;
case 'B':
args.B = atoi(optarg);
if(args.B<=0) {fprintf(stderr,"The option -B must be a positve number\n");exit(1);}
break;
case 'h':
explain_command(argv);
exit(0);
case '?': /* getopt_long already printed an error message. */
exit(1);
break;
default:
abort ();
}
}
if (argc - optind!=2&&args.inbin_file==NULL){
explain_command(argv); exit(1);
}
if(args.inbin_file==NULL){
args.tumor_file = strdup(argv[optind]);
args.normal_file = strdup(argv[optind+1]);
args.in_tmor = fopen(args.tumor_file,"r");
if(args.in_tmor == NULL)
{ fprintf(stderr,"fopen %s: %s\n", args.tumor_file,strerror(errno));
exit(1);
}
args.in_nml = fopen(args.normal_file,"r");
if(args.in_nml == NULL)
{ fprintf(stderr,"fopen %s: %s\n", args.normal_file,strerror(errno));
exit(1);
}
}
else{
args.inbin = fopen(args.inbin_file,"r");
if(args.inbin==NULL){
fprintf(stderr,"fopen %s: %s\n", args.inbin_file,strerror(errno));
exit(1);
}
}
if(args.outlier_file!=NULL) {
args.outlier = fopen(args.outlier_file,"w");
if(args.outlier==NULL) {fprintf(stderr,"fopen %s: %s\n",args.outlier_file,strerror(errno));exit(1);}
}
if(args.output_file!=NULL){
args.output = fopen(args.output_file,"w");
if(args.output==NULL) { fprintf(stderr,"fopen %s: cannot create the file.\n",args.output_file); exit(1);}
}else{
args.output = stdout;
}
if(args.binout_file!=NULL){
args.outbin = fopen(args.binout_file,"w");
if(args.outbin==NULL) { fprintf(stderr,"fopen %s: cannot create the file.\n",args.binout_file); exit(1);}
}
if(insert!=NULL){
char *substr;
substr = strtok(insert,",");
args.insert = atoi(substr);
substr=strtok(NULL,",");
if(substr==NULL){fprintf(stderr,"Incorrect format for option -I\n");exit(1);}
args.sd = atoi(substr);
if(args.insert<0||args.sd<0) {fprintf(stderr,"Error, insert size and its standard deviaiton must be positive\n");}
}
set_lambda(args.lambda);
return args;
}