void test_push_bcf_gt_md(void)
{
pri_queue q = priq_new(0);
struct bcf_file bcf_f = init_bcf_file(BCF_FILE);
uint64_t *md_index = (uint64_t *) malloc(NUM_VARS * sizeof(uint64_t));
char *gt_of_name = "tmp.gt_of_name";
char *md_of_name = "tmp.md_of_name";
push_bcf_gt_md(&q,
&bcf_f,
md_index,
NUM_INDS,
NUM_VARS,
gt_of_name,
md_of_name);
FILE *f = fopen(gt_of_name, "rb");
//remove(gt_of_name);
//remove(md_of_name);
free(md_index);
}
//{{{ void print_query_result_offset(uint32_t *mask,
void print_query_result_offset(uint32_t *mask,
uint32_t mask_len,
uint32_t *vids,
struct gqt_query *q,
uint32_t **counts,
uint32_t *id_lens,
uint32_t *U_R,
uint32_t U_R_len,
char **id_query_list,
char **gt_query_list,
uint32_t num_qs,
uint32_t num_fields,
char *off_file_name,
char *source_file,
char *full_cmd)
{
struct off_file *off_f = open_off_file(off_file_name);
struct bcf_file bcf_f = init_bcf_file(source_file);
char *sample_names = NULL;
uint32_t i,j,k,line_idx,bytes, bit_i = 0;
int r;
for (i = 0; i < U_R_len; ++i) {
if (i == 0 )
r = asprintf(&sample_names,
"%s",
bcf_f.hdr->samples[U_R[i]]);
else
r = asprintf(&sample_names,
"%s,%s",
sample_names,
bcf_f.hdr->samples[U_R[i]]);
if (r == -1)
err(EX_OSERR, "asprintf error");
}
if (bcf_hdr_set_samples(bcf_f.hdr, sample_names, 0) != 0)
errx(EX_DATAERR, "Error setting samples: %s\n", source_file);
char *info_s;
for (i = 0; i < num_qs; i++) {
if ( q[i].variant_op == p_count ) {
r = asprintf(&info_s, "##INFO=<ID=GQT_%u,Number=1,Type=Integer,"
"Description=\"GQT count result from "
"phenotype:'%s' genotype:'%s'\">",
i, id_query_list[i], gt_query_list[i]);
if (r == -1) err(EX_OSERR, "asprintf error");
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
} else if ( q[i].variant_op == p_pct ) {
r = asprintf(&info_s, "##INFO=<ID=GQT_%u,Number=1,Type=Float,"
"Description=\"GQT percent result from "
"phenotype:'%s' genotype:'%s'\">",
i, id_query_list[i], gt_query_list[i]);
if (r == -1) err(EX_OSERR, "asprintf error");
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
} else if ( q[i].variant_op == p_maf ) {
r = asprintf(&info_s, "##INFO=<ID=GQT_%u,Number=1,Type=Float,"
"Description=\"GQT maf result from "
"phenotype:'%s' genotype:'%s'\">",
i, id_query_list[i], gt_query_list[i]);
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
}
}
r = asprintf(&info_s, "##%s_queryVersion=%s", PROGRAM_NAME, VERSION);
if (r == -1) err(EX_OSERR, "asprintf error");
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
r = asprintf(&info_s, "##%s_queryCommand=%s", PROGRAM_NAME, full_cmd);
if (r == -1) err(EX_OSERR, "asprintf error");
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
htsFile *out_f = hts_open("-","w");
if ( !out_f )
err(EX_DATAERR, "Could open output file");
bcf_hdr_write(out_f, bcf_f.hdr);
bcf_f.line = bcf_init1();
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;
r = goto_bcf_line(&bcf_f, off_f, line_idx);
if (r == -1)
err(EX_NOINPUT,
"Error seeking file '%s'", bcf_f.file_name);
r = get_bcf_line(&bcf_f);
if (r == -1)
err(EX_NOINPUT,
"Error reading file '%s'", bcf_f.file_name);
for (k=0; k < num_qs; k++) {
r = asprintf(&info_s, "GQT_%u", k);
if (r == -1)
err(EX_OSERR, "asprintf error");
if ( q[k].variant_op == p_count ) {
int32_t v = counts[k][line_idx];
if (bcf_update_info_int32(bcf_f.hdr,
bcf_f.line,
info_s,
&v,
1) != 0)
errx(EX_DATAERR,
"Error adding to info field: %s\n",
bcf_f.file_name);
} else if (q[k].variant_op == p_pct) {
float v = ((float)counts[k][line_idx])/
((float) id_lens[k]);
if (bcf_update_info_float(bcf_f.hdr,
bcf_f.line,
info_s,
&v,
1) != 0)
errx(EX_DATAERR,
"Error adding to info field: %s\n",
bcf_f.file_name);
} else if (q[k].variant_op == p_maf) {
float v = ((float)counts[k][line_idx])/
(((float) id_lens[k])*2.0);
if (bcf_update_info_float(bcf_f.hdr,
bcf_f.line,
info_s,
&v,
1) != 0)
errx(EX_DATAERR,
"Error adding to info field: %s\n",
bcf_f.file_name);
}
}
bcf_write(out_f, bcf_f.hdr, bcf_f.line);
}
bit_i++;
if (bit_i == num_fields)
break;
}
if (bit_i == num_fields)
break;
}
hts_close(out_f);
destroy_off_file(off_f);
}
//{{{void test_init_bcf_file_remote(void)
void test_init_bcf_file_remote(void)
{
char *remote_file = "http://s3-us-west-2.amazonaws.com/gqt-data/test/10.1e4.var.bcf";
struct bcf_file rbf = init_bcf_file(remote_file);
}
void test_init_bcf_file(void)
{
struct bcf_file bcf_f = init_bcf_file(BCF_FILE);
TEST_ASSERT_EQUAL(NUM_INDS, bcf_f.num_records);
close_bcf_file(&bcf_f);
}
