void type_ext2_inode___file (char *command_line)
{
char buffer [80];
if (!S_ISREG (type_data.u.t_ext2_inode.i_mode)) {
wprintw (command_win,"Error - Inode type is not file\n");refresh_command_win ();
return;
}
if (!init_file_info ()) {
wprintw (command_win,"Error - Unable to show file\n");refresh_command_win ();
return;
}
sprintf (buffer,"settype file");dispatch (buffer);
}
static int start_server(struct server *s)
{
WSADATA wsadata;
WSAStartup(MAKEWORD(2,2), &wsadata);
s->udp_port = connect_udp(s->sd);
if(s->udp_port < 0) {
fprintf(stderr, "Failed to open UDP port\n");
return -1;
}
init_file_info(&s->finfo);
if(pthread_create(&s->tid, NULL, &message_thread, s) < 0) {
perror("pthread_create");
close(s->sd[0]);
close(s->sd[1]);
return -1;
}
return 0;
}
void onAccept(int sockfd)
{
char receive_buffer[RECEIVE_BUFFER_SIZE]={0,};
recv(sockfd,receive_buffer,RECEIVE_BUFFER_SIZE,0);
printf("%s\n",receive_buffer);
uufile_t req_file_info;
init_file_info(&req_file_info);
get_requested_file_info(receive_buffer,&req_file_info);
int need_buffer_size = SEND_BUFFER_SIZE;
if(( FILE_TEXT == req_file_info.type) || (FILE_BINARY == req_file_info.type)){
need_buffer_size = req_file_info.size;
}
char *send_buffer=(char *)malloc((need_buffer_size)*sizeof(char));
if(send_buffer != NULL){
memset(send_buffer,0,need_buffer_size);
if( OP_SUCCESS == handle_request_file(&req_file_info,send_buffer,SEND_BUFFER_SIZE)){
send(sockfd,send_buffer,req_file_info.size,0);
}
free(send_buffer);
}
}
void merge_vcf(int n_vcf, char **vcf_filenames) {
FileInfo *f_info;
int n_done, n_chrom, i, *is_lowest, *lowest, n_lowest;
int ret, use_geno_probs, use_haplotypes;
Chromosome *chrom_tab;
f_info = init_file_info(n_vcf, vcf_filenames);
/* find chromosomes that are present in ALL VCFs */
chrom_tab = chrom_table_intersect(f_info, n_vcf, &n_chrom);
n_done = 0;
is_lowest = my_malloc(sizeof(int) * n_vcf);
lowest = my_malloc(sizeof(int) * n_vcf);
/* only use genotypes and haplotypes if they are present in ALL files */
use_geno_probs = TRUE;
use_haplotypes = TRUE;
/* read first SNP from all files */
for(i = 0; i < n_vcf; i++) {
ret = vcf_read_line(f_info[i].gzf, f_info[i].vcf, &f_info[i].cur_snp);
if(ret == -1) {
/* file is over */
n_done += 1;
f_info[i].is_done = TRUE;
my_warn("file %s contains no SNPs\n", vcf_filenames[i]);
f_info[i].cur_chrom = NULL;
} else {
set_cur_chrom(&f_info[i], chrom_tab, n_chrom);
if(!f_info[i].cur_snp.has_geno_probs) {
if(use_geno_probs) {
fprintf(stderr, "Not using genotype likelihoods (GL) because "
"not present in file %s\n", vcf_filenames[i]);
}
use_geno_probs = FALSE;
}
if(!f_info[i].cur_snp.has_haplotypes) {
if(use_haplotypes) {
fprintf(stderr, "Not using genotypes (GT) because "
"not present in file %s\n", vcf_filenames[i]);
}
use_haplotypes = FALSE;
}
}
}
fprintf(stderr, "parsing files\n");
while(n_done < n_vcf) {
/* find SNP(s) with lowest (chrom, pos) */
find_lowest(f_info, n_vcf, is_lowest, lowest, &n_lowest);
/* merge counts and write line for these SNPs */
write_output(stdout, f_info, n_vcf, is_lowest, lowest,
use_geno_probs, use_haplotypes);
/* advance files with lowest SNPs */
for(i = 0; i < n_vcf; i++) {
if(!f_info[i].is_done && is_lowest[i]) {
if(vcf_read_line(f_info[i].gzf, f_info[i].vcf, &f_info[i].cur_snp) == -1) {
/* have reached end of this file */
n_done += 1;
f_info[i].is_done = TRUE;
}
}
}
}
fprintf(stderr, "done!\n");
free_file_info(f_info, n_vcf);
for(i = 0; i < n_chrom; i++) {
my_free(chrom_tab[i].name);
my_free(chrom_tab[i].assembly);
}
my_free(chrom_tab);
my_free(is_lowest);
}
