void server_run() {
int filedes,filed,size,numbofargs,i,jsize=0,jobID=0,digit_count = 0,num,status,N,id;
pid_t cpid,commpid,stopid;
char *buffer;
char *temp;
char *command;
char *jobname;
char *str;
char **args;
static struct sigaction act;
act.sa_handler = handler;
sigfillset(&(act.sa_mask));
sigaction(SIGRTMIN, &act, NULL);
static struct sigaction chd;
chd.sa_handler = child_handler;
sigfillset(&(chd.sa_mask));
sigaction(SIGCHLD, &chd, NULL);
if (( filedes = open("server", O_CREAT | O_RDWR , 0666))== -1) {
perror (" creating ");
exit (3) ;
}
cpid = getpid();
num = cpid;
digit_count += no_of_digits(num);
str = malloc(sizeof(char)*(digit_count+1));//to str einai ena string pou exei mesa to pid tou server
str[digit_count] = '\0';
while(num > 0){
str[digit_count-1] = num%10 + '0';
num = num/10;
digit_count--;
}
if ((write(filedes,str,sizeof(strlen(str)+1))) == -1) {
perror ("Error in Writing ");
exit (4) ;
}
free(str);
if ((filed = open("myfifo",O_RDWR)) <0 ){
perror (" fifo open problem ");
exit(8);
}
list_create();
kill(getppid(),SIGRTMIN);
while (1) {
flag = 0;
while (flag == 0)
sleep(1);
jsize = 0;
read(filed,&commpid,sizeof(pid_t));
read(filed,&numbofargs,sizeof(int));
args = (char**)malloc(numbofargs*sizeof(char*));
read(filed,&size,sizeof(int));
buffer = (char *)malloc(size);
read(filed,buffer,size);
temp = (char *)malloc(size);
strcpy(temp,buffer);
command = strtok(temp," ");//pairnw thn entolh(issuejob,poll klp)
for (i=0;i<numbofargs;i++) {
args[i] = strtok(NULL," ");
jsize += strlen(args[i])+1;//kai ta argument auths
}
jsize += 1;
jobname = (char *)malloc(jsize);
jobname[0] = '\0';
for (i=0;i<numbofargs;i++) {
strcat(jobname,args[i]);
strcat(jobname," ");
}
if (strcmp(command,"issuejob") == 0) {
if (args[0] == NULL) {//se periptwsh pou den dwthei argument meta to issuejob
free(args);
free(temp);
free(buffer);
free(jobname);
continue;
}
jobID++;
issuejob(args,numbofargs,jobname,jobID,&status);
write(filed,&jobID,sizeof(int));
write(filed,&status,sizeof(int));
write(filed,&jsize,sizeof(int));
write(filed,jobname,jsize);
kill(commpid,SIGRTMIN);
}
else if (strcmp(command,"setConcurrency") == 0) {
if (args[0] == NULL) {
free(args);
free(temp);
free(buffer);
free(jobname);
continue;
}
N = atoi(args[0]);
setConcurrency(N);
}
else if (strcmp(command,"stop") == 0) {
if (args[0] == NULL) {
free(args);
free(temp);
free(buffer);
free(jobname);
continue;
}
id = atoi(args[0]);
search_and_delete(id,&stopid);
if (stopid != 0)
kill(stopid,SIGKILL);
}
else if (strcmp(command,"poll") == 0) {
if (args[0] == NULL) {
free(args);
free(temp);
free(buffer);
free(jobname);
continue;
}
if (strcmp(args[0],"running") == 0)
poll(1,filed);
else if (strcmp(args[0],"queued") == 0)
poll(0,filed);
else {
free(args);
free(temp);
free(buffer);
free(jobname);
continue;
}
kill(commpid,SIGRTMIN);
}
else if (strcmp(command,"exit") == 0) {
queued_delete_all();//sbinw olh th lista anamonhs
free(args);
free(temp);
free(buffer);
free(jobname);
while (get_running_jobs() != 0)//kai prin kleisei o server perimenw na teleiwsoun oles oi running jobs
sleep(1);
break;
}
free(args);
free(temp);
free(buffer);
free(jobname);
}
list_destroy();
remove("server");
remove("myfifo");
}
loci_stats *bam_access_get_position_base_counts(char *chr, int posn){
char *region = NULL;
hts_itr_t *iter = NULL;
bam1_t* b = NULL;
bam_plp_t buf;
loci_stats *stats = malloc(sizeof(loci_stats *));
check_mem(stats);
stats->base_counts = malloc(sizeof(int) * 4);
check_mem(stats->base_counts);
stats->base_counts[0] = 0;
stats->base_counts[1] = 0;
stats->base_counts[2] = 0;
stats->base_counts[3] = 0;
fholder->stats = stats;
region = malloc((sizeof(char *) * (strlen(chr)+1))+sizeof(":")+sizeof("-")+(sizeof(char)*((no_of_digits(posn)*2)+1)));
sprintf(region,"%s:%d-%d",chr,posn,posn);
fholder->beg = posn;
fholder->end = posn;
// initialize pileup
buf = bam_plp_init(pileup_func, (void *)fholder);
bam_plp_set_maxcnt(buf,maxitercnt);
/*
sam_fetch(fholder->in, fholder->idx, ref, fholder->beg, fholder->end, buf, fetch_algo_func);
*/
//Replace fetch with iterator for htslib compatibility.
b = bam_init1();
iter = sam_itr_querys(fholder->idx, fholder->head, region);
int result;
int count = 0;
while ((result = sam_itr_next(fholder->in, iter, b)) >= 0) {
if(b->core.qual < min_map_qual || (b->core.flag & BAM_FUNMAP)
|| !(b->core.flag & BAM_FPROPER_PAIR) || (b->core.flag & BAM_FMUNMAP)//Proper pair and mate unmapped
|| (b->core.flag & BAM_FDUP)//1024 is PCR/optical duplicate
|| (b->core.flag & BAM_FSECONDARY) || (b->core.flag & BAM_FQCFAIL)//Secondary alignment, quality fail
|| (b->core.flag & BAM_FSUPPLEMENTARY) ) continue;
count++;
bam_plp_push(buf, b);
}
sam_itr_destroy(iter);
bam_plp_push(buf, 0);
int tid, pos, n_plp = -1;
const bam_pileup1_t *pil;
while ( (pil=bam_plp_next(buf, &tid, &pos, &n_plp)) > 0) {
if((pos+1) != posn) continue;
int i=0;
for(i=0;i<n_plp;i++){
const bam_pileup1_t *p = pil + i;
int qual = bam_get_qual(p->b)[p->qpos];
uint8_t c = bam_seqi(bam_get_seq(p->b), p->qpos);
if(!(p->is_del) && qual >= min_base_qual
&& p->b->core.qual >= min_map_qual){
//&& (c == 1 /*A*/|| c == 2 /*C*/|| c == 4 /*G*/|| c == 8 /*T*/)){
//Now we add a new read pos struct to the list since the read is valid.
//char cbase = toupper(bam_nt16_rev_table[c]);
switch(c){
case 1:
fholder->stats->base_counts[0]++;
break;
case 2:
fholder->stats->base_counts[1]++;
break;
case 4:
fholder->stats->base_counts[2]++;
break;
case 8:
fholder->stats->base_counts[3]++;
break;
default:
break;
}; // End of args switch statement */
}
}
} //End of iteration through pileup
//bam_plp_push(buf, 0); // finalize pileup
bam_plp_destroy(buf);
free(region);
return fholder->stats;
error:
//if(region) free(region);
if(fholder->stats){
if(fholder->stats->base_counts) free(fholder->stats->base_counts);
free(fholder->stats);
}
if(iter) sam_itr_destroy(iter);
if(b) bam_destroy1(b);
if(region) free(region);
return NULL;
}