/*
signal handler with SA_SIGINFO - redirects to registered signals
*/
static void signal_handler_info(int signum, siginfo_t *info, void *uctx)
{
uint32_t count = sig_count(sig_state->signal_count[signum]);
sig_state->sig_info[signum][count] = *info;
signal_handler(signum);
/* handle SA_SIGINFO */
if (count+1 == SA_INFO_QUEUE_COUNT) {
/* we've filled the info array - block this signal until
these ones are delivered */
sigset_t set;
sigemptyset(&set);
sigaddset(&set, signum);
sigprocmask(SIG_BLOCK, &set, NULL);
SIG_INCREMENT(sig_state->sig_blocked[signum]);
}
}
int main (int argc, char *argv[])
{
argument_read(&argc, argv, args);//reading arguments
if (filesmt == NULL || filesig == NULL || sigfmt == NULL || region_mode == NULL) usage();
struct chr_block *chr_block_headsmt = NULL; //for summit
struct chr_block *chr_block_headsig = NULL; //for signal
struct chr_block *chr_block_headsig_d = NULL; //for signal of denominator
struct chr_block *ch; //for "for loop of chr"
struct output *output_head = NULL; //for output
/*path, filename, and extension*/
char path_smt[PATH_STR_LEN] = {0};
char fn_smt[FILE_STR_LEN] = {0};
char ext_smt[EXT_STR_LEN] = {0};
char path_sig[PATH_STR_LEN] = {0};
char fn_sig[FILE_STR_LEN] = {0};
char ext_sig[EXT_STR_LEN] = {0};
char path_sig_d[PATH_STR_LEN] = {0};
char fn_sig_d[FILE_STR_LEN] = {0};
char ext_sig_d[EXT_STR_LEN] = {0};
char output_name[PATH_STR_LEN + FILE_STR_LEN + EXT_STR_LEN] = {0}; //output file name
time_t timer;
if(hf) strcpy(hfs, "on\0");
if(nf) strcpy(nfs, "on\0");
time(&timer);
printf("Tool: %s\n\n\
Input file summit: %s\n\
Input file signal: %s\n\
Input file signal denominator: %s\n\
signal format: %s\n\
region mode: %s\n\
summit col of chr, start, end: %d, %d, %d\n\
summit col of summit: %d\n\
summit col strand?: %d\n\
half range: %d\n\
header flag: %s\n\
norm by length flag: %s\n\
time: %s\n",\
"ga_reads_region", filesmt, filesig, filesig_d, sigfmt, region_mode, col_chr, col_st, col_ed, col_st, col_strand, hw, hfs, nfs, ctime(&timer) );
ga_parse_file_path (filesmt, path_smt, fn_smt, ext_smt); //parsing input file name into path, file name, and extension
ga_parse_file_path (filesig, path_sig, fn_sig, ext_sig);
ga_parse_chr_bs(filesmt, &chr_block_headsmt, col_chr, col_st, col_ed, col_strand, hf); //parsing each binding sites for each chromosome
// reading signal file
if (!strcmp(sigfmt, "bedgraph")) {
ga_parse_bedgraph (filesig, &chr_block_headsig);
} else if (!strcmp(sigfmt, "sepwiggz")) {
ga_parse_sepwiggz (filesig, &chr_block_headsig);
} else if (!strcmp(sigfmt, "onewiggz")) {
ga_parse_onewiggz (filesig, &chr_block_headsig);
} else {
LOG("error: invalid signal file format.");
goto err;
}
// sorting summit and sig
chr_block_headsmt = ga_mergesort_chr(chr_block_headsmt);
chr_block_headsig = ga_mergesort_chr(chr_block_headsig);
for (ch = chr_block_headsmt; ch; ch = ch -> next) {
ch -> bs_list = ga_mergesort_bs(ch -> bs_list);
}
for (ch = chr_block_headsig; ch; ch = ch -> next) {
ch -> sig_list = ga_mergesort_sig(ch -> sig_list);
}
if (filesig_d) {//if denominator
ga_parse_file_path (filesig_d, path_sig_d, fn_sig_d, ext_sig_d);
if (!strcmp(sigfmt, "bedgraph")) {
ga_parse_bedgraph (filesig_d, &chr_block_headsig_d);
} else if (!strcmp(sigfmt, "sepwiggz")) {
ga_parse_sepwiggz (filesig_d, &chr_block_headsig_d);
} else if (!strcmp(sigfmt, "onewiggz")) {
ga_parse_onewiggz (filesig_d, &chr_block_headsig_d);
} else {
LOG("error: invalid signal file format.");
goto err;
}
chr_block_headsig_d = ga_mergesort_chr(chr_block_headsig_d); //sorting chr of sig
for (ch = chr_block_headsig_d; ch; ch = ch -> next) {
ch -> sig_list = ga_mergesort_sig(ch -> sig_list); //sorting sig
}
}
if (sig_count (chr_block_headsmt, chr_block_headsig, chr_block_headsig_d, &output_head) != 0) {
LOG("error: in sig_count function.");
goto err;
}
if (filesig_d) { //if denominator
if (!strcmp(region_mode, "region")) sprintf(output_name, "%s%s_around_%s_mode_%s_divided_%s.txt", path_sig, fn_sig, fn_smt, region_mode, fn_sig_d);
else sprintf(output_name, "%s%s_around_%s_halfwid%d_mode_%s_divided_%s.txt", path_sig, fn_sig, fn_smt, hw, region_mode, fn_sig_d);
} else {
if (!strcmp(region_mode, "region")) sprintf(output_name, "%s%s_around_%s_mode_%s.txt", path_sig, fn_sig, fn_smt, region_mode);
else sprintf(output_name, "%s%s_around_%s_halfwid%d_mode_%s.txt", path_sig, fn_sig, fn_smt, hw, region_mode);
}
if (ga_header_line != NULL) { //if header line
if (add_one_val(ga_line_out, ga_header_line, "signal_region\n") < 0) {
LOG("error: output line was too long.");
goto err; //adding one extra column
}
ga_write_lines (output_name, output_head, ga_line_out); //note that header is line_out, not ga_header_line
}
else ga_write_lines (output_name, output_head, ga_header_line);
goto rtfree;
rtfree:
MYFREE (ga_header_line);
if (chr_block_headsmt) ga_free_chr_block(&chr_block_headsmt);
if (chr_block_headsig) ga_free_chr_block(&chr_block_headsig);
if (chr_block_headsig_d) ga_free_chr_block(&chr_block_headsig_d);
if (output_head) ga_free_output(&output_head);
return 0;
err:
MYFREE (ga_header_line);
if (chr_block_headsmt) ga_free_chr_block(&chr_block_headsmt);
if (chr_block_headsig) ga_free_chr_block(&chr_block_headsig);
if (chr_block_headsig_d) ga_free_chr_block(&chr_block_headsig_d);
if (output_head) ga_free_output(&output_head);
return -1;
}
