void print_count_result(uint32_t *R,
uint32_t num_fields,
char *bim)
{
struct quick_file_info qfile;
struct output_buffer out_buf;
size_t i=0;
if (bim != NULL) {
quick_file_init(bim, &qfile);
}
init_out_buf(&out_buf, NULL);
for(; i < num_fields; ++i) {
if (bim != NULL) {
append_out_buf(&out_buf, qfile.lines[i], qfile.line_lens[i]);
}
append_out_buf(&out_buf, "\t", 1);
append_integer_to_out_buf(&out_buf, R[i]);
append_out_buf(&out_buf, "\n", 1);
}
append_out_buf(&out_buf, "\n", 1);
quick_file_delete(&qfile);
free_out_buf(&out_buf);
}
//{{{ void print_query_result_bim(uint32_t *mask,
void print_query_result_bim(uint32_t *mask,
uint32_t mask_len,
uint32_t *vids,
struct gqt_query *q,
uint32_t **counts,
uint32_t *id_lens,
uint32_t num_qs,
uint32_t num_fields,
char *bim,
char *full_cmd)
{
uint32_t i,j,k,line_idx,bytes, bit_i = 0;
struct quick_file_info qfile;
struct output_buffer outbuf;
char pct[50];
init_out_buf(&outbuf, NULL);
quick_file_init(bim, &qfile);
append_out_buf(&outbuf,
qfile.main_buf,
qfile.header_len);
char *info_s = NULL;;
int r = asprintf(&info_s,
"##%s_queryVersion=%s\n"
"##%s_queryCommand=%s\n",
PROGRAM_NAME, VERSION,
PROGRAM_NAME, full_cmd);
if (r == -1) err(EX_OSERR, "asprintf error");
append_out_buf(&outbuf, info_s, strlen(info_s));
for (k=0; k < num_qs; k++) {
if ( q[k].variant_op == p_count ) {
r = asprintf(&info_s, "##INFO=<ID=GQT_%u,Number=1,Type=Integer,"
"Description=\"GQT count result from query "
"%u\">\n",
k, k);
if (r == -1) err(EX_OSERR, "asprintf error");
append_out_buf(&outbuf, info_s, strlen(info_s));
} else if ( q[k].variant_op == p_pct ) {
r = asprintf(&info_s, "##INFO=<ID=GQT_%u,Number=1,Type=Float,"
"Description=\"GQT percent result from query "
"%u\">\n",
k, k);
if (r == -1) err(EX_OSERR, "asprintf error");
append_out_buf(&outbuf, info_s, strlen(info_s));
} else if ( q[k].variant_op == p_maf ) {
r = asprintf(&info_s, "##INFO=<ID=GQT_%u,Number=1,Type=Float,"
"Description=\"GQT maf result from query "
"%u\">\n",
k, k);
if (r == -1) err(EX_OSERR, "asprintf error");
append_out_buf(&outbuf, info_s, strlen(info_s));
}
}
char last_header_line[]="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
append_out_buf(&outbuf, last_header_line, strlen(last_header_line));
for (i=0; i < mask_len; ++i) {
bytes = mask[i];
if (bytes == 0)
continue; /* skip a bunch of ops if you can */
for (j=0; j < 32; j++) {
if (bytes & 1 << (31 - j)) {
line_idx = i*32+j;
append_out_buf(&outbuf,
qfile.lines[line_idx],
qfile.line_lens[line_idx]-1);
for (k=0; k < num_qs; k++) {
if ( q[k].variant_op == p_count ) {
r = asprintf(&info_s,
";GQT_%u=%u",
k,
counts[k][line_idx]);
//counts[k][vids[line_idx]]);
if (r == -1) err(EX_OSERR, "asprintf error");
append_out_buf(&outbuf, info_s, strlen(info_s));
} else if (q[k].variant_op == p_pct) {
r = asprintf(&info_s, ";GQT_%u=%f", k,
//((float)counts[k][vids[line_idx]])/
((float)counts[k][line_idx])/
((float) id_lens[k]));
if (r == -1) err(EX_OSERR, "asprintf error");
append_out_buf(&outbuf, info_s, strlen(info_s));
} else if (q[k].variant_op == p_maf) {
r = asprintf(&info_s, ";GQT_%u=%f", k,
//((float)counts[k][vids[line_idx]])/
((float)counts[k][line_idx])/
(((float) id_lens[k])*2.0));
if (r == -1) err(EX_OSERR, "asprintf error");
append_out_buf(&outbuf, info_s, strlen(info_s));
}
}
append_out_buf(&outbuf,"\n",1);
}
bit_i++;
if (bit_i == num_fields)
break;
}
if (bit_i == num_fields)
break;
}
quick_file_delete(&qfile);
free_out_buf(&outbuf);
}
void print_result(unsigned int len,
unsigned int *R,
unsigned int num_fields,
char *bim)
{
/* OLD WAY *********************
unsigned int i,j, bit_i = 0;
for(i = 0; i < len; ++i) {
if (i!= 0)
printf(" ");
int *r = unpack_1_bit_ints(R[i]);
for(j = 0; j < 32; ++j) {
if (j!= 0)
printf(" ");
printf("%d", r[j]);
bit_i += 1;
if (bit_i == num_fields)
break;
}
if (bit_i == num_fields)
break;
free(r);
}
printf("\n");
NEW WAY */
unsigned int i,j,line_idx,bytes, bit_i = 0;
struct quick_file_info qfile;
struct output_buffer outbuf;
init_out_buf(&outbuf, NULL);
quick_file_init(bim, &qfile);
for (i=0; i < len; ++i) {
bytes = R[i];
if (bytes == 0) continue; /* skip a bunch of ops if you can */
for (j=0; j < 32; j++) {
if (bytes & 1 << (31 - j)) {
line_idx = i*32+j;
append_out_buf(&outbuf, qfile.lines[line_idx], qfile.line_lens[line_idx]);
append_out_buf(&outbuf,"\n",1);
}
bit_i++;
if (bit_i == num_fields)
break;
}
if (bit_i == num_fields)
break;
}
quick_file_delete(&qfile);
free_out_buf(&outbuf);
}