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stix.c
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#define _GNU_SOURCE
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <getopt.h>
#include <sysexits.h>
#include <err.h>
#include <sqlite3.h>
#include <htslib/hfile.h>
#include <htslib/vcf.h>
#include "ped.h"
#include "search.h"
#include "sharding_utils.h"
char *stix_sv_type_strings[5] = {"DEL", "DUP", "INS", "INV", "BND"};
uint32_t parse_aggregate_csv(char *aggregate,
char ***agg_cols);
void print_results(struct giggle_index *gi,
char *ped_db_file_name,
struct stix_breakpoint *left,
struct stix_breakpoint *right,
uint32_t *sample_ids,
char *filter,
struct uint_pair *sample_alt_depths,
uint32_t num_samples,
char **agg_cols,
uint32_t num_agg_cols,
uint32_t json_out,
uint32_t summary_only,
uint32_t depths_only);
void update_vcf_header(bcf_hdr_t *hdr,
uint32_t v_is_set,
char *sample_column);
//{{{int help(int exit_code)
int help(int exit_code)
{
fprintf(stderr,
"STIX: Structural Variant Index\n"
"Version: 2.0.0\n"
"usage: stix <options>\n"
" options:\n"
" -i index directory\n"
" -s slop\n"
" -P padding base piars for query insertion(default 50)\n"
" -p PED file\n"
" -B Sharding file (giggle_index \\t STIX_index)\n"
" -Q Batch queries in table format (left \\t right \\t len \\t SVtype \\t ID)\n"
" -T Threshold to define STIX_ONE (number of supporting reads required to define a hit) (default: 1)\n"
" -c Alt file column (default 1)\n"
" -d PED database file\n"
" -r right SV region\n"
" -l left SV region\n"
" -f VCF file\n"
" -a List of columns to aggregate over\n"
" -F Filter samples by PED field query\n"
" -j JSON output\n"
" -t SV type (DEL,INS,INV,DUP,BND) \n"
" -L Length of Insertion(use it when -t INS) \n"
" -R Relative Erorr Threshold to compare the length of query INS and targeted INS (0.0-1.0) (default:0.15) \n"
" -v Add sample depth to VCF file\n"
" -S Give only summary\n"
" -D Give sample depth array\n"
" -V Verbose mode(print debug information, will increase output file size greatly)\n");
return exit_code;
}
//}}}
//{{{void print_results(struct giggle_index *gi,
void print_results(struct giggle_index *gi,
char *ped_db_file_name,
struct stix_breakpoint *left,
struct stix_breakpoint *right,
uint32_t *sample_ids,
char *filter,
struct uint_pair *sample_alt_depths,
uint32_t num_samples,
char **agg_cols,
uint32_t num_agg_cols,
uint32_t json_out,
uint32_t summary_only,
uint32_t depths_only)
{
uint32_t i;
uint32_t num_col_vals;
int32_t zero_count, one_count;
uint32_t Q1, Q2, Q3, min, max;
int32_t counts[4];
uint32_t ret = stix_get_summary(sample_alt_depths,
sample_ids,
num_samples,
&zero_count,
&one_count,
&Q1,
&Q2,
&Q3,
&min,
&max,
counts);
if (json_out == 1)
printf("{ \"results\": {\n");
if (json_out == 1)
{
printf("\"summary\": [\n");
printf("{"
"\"name\":\"Total\", "
"\"zero_count\":\"%d\", "
"\"one_count\":\"%d\","
"\"quantiles\":[\"%u\",\"%u\",\"%u\"], "
"\"counts\":[\"%u\",\"%u\",\"%u\",\"%u\"]",
zero_count,
one_count,
Q1, Q2, Q3,
counts[0], counts[1], counts[2], counts[3]);
}
else
{
printf("Total\t0:1\t%d:%d\t%u:%u:%u\t%d:%d:%d:%d",
zero_count, one_count,
Q1, Q2, Q3,
counts[0], counts[1], counts[2], counts[3]);
}
if (depths_only == 1)
{
uint32_t *sample_depths = NULL;
ret = stix_get_sample_depths(sample_alt_depths,
NULL,
num_samples,
&sample_depths);
if (json_out == 0)
{
for (i = 0; i < num_samples; ++i)
printf("\t%d", sample_depths[i]);
}
else
{
printf(",\"depths\":[");
for (i = 0; i < num_samples; ++i)
{
if (i != 0)
printf(",");
printf("%d", sample_depths[i]);
}
printf("]");
}
free(sample_depths);
}
if (json_out == 1)
printf("}");
printf("\n");
sqlite3 *db = NULL;
if (num_agg_cols > 0)
{
char ***uniq_vals;
uint32_t num_uniq_vals;
uint32_t **uniq_groups_ids;
uint32_t *uniq_groups_sizes;
num_uniq_vals = ped_get_uniq_col_groups(ped_db_file_name,
&db,
agg_cols,
num_agg_cols,
filter,
&uniq_vals,
&uniq_groups_ids,
&uniq_groups_sizes);
for (i = 0; i < num_uniq_vals; ++i)
{
uint32_t j;
char *group_name_tmp, *group_name;
ret = asprintf(&group_name, "%s", uniq_vals[i][0]);
for (j = 1; j < num_agg_cols; ++j)
{
ret = asprintf(&group_name_tmp,
"%s,%s",
group_name,
uniq_vals[i][j]);
free(group_name);
group_name = group_name_tmp;
}
ret = stix_get_summary(sample_alt_depths,
uniq_groups_ids[i],
uniq_groups_sizes[i],
&zero_count,
&one_count,
&Q1,
&Q2,
&Q3,
&min,
&max,
counts);
if (json_out)
{
printf(",{"
"\"name\":\"%s\", "
"\"zero_count\":\"%d\", "
"\"one_count\":\"%d\","
"\"quantiles\":[\"%u\",\"%u\",\"%u\"], "
"\"counts\":[\"%u\",\"%u\",\"%u\",\"%u\"]",
group_name,
zero_count,
one_count,
Q1, Q2, Q3,
counts[0], counts[1], counts[2], counts[3]);
}
else
{
printf("%s\t0:1\t%d:%d\t%u:%u:%u\t%d:%d:%d:%d",
group_name,
zero_count, one_count,
Q1, Q2, Q3,
counts[0], counts[1], counts[2], counts[3]);
}
if (depths_only == 1)
{
uint32_t *sample_depths = NULL;
ret = stix_get_sample_depths(sample_alt_depths,
uniq_groups_ids[i],
uniq_groups_sizes[i],
&sample_depths);
int k;
if (json_out == 0)
{
for (k = 0; k < uniq_groups_sizes[i]; ++k)
printf("\t%d", sample_depths[k]);
}
else
{
printf(",\"depths\":[");
for (k = 0; k < uniq_groups_sizes[i]; ++k)
{
if (k != 0)
printf(",");
printf("%d", sample_depths[k]);
}
printf("]");
}
free(sample_depths);
}
if (json_out == 1)
printf("}");
printf("\n");
free(group_name);
}
}
if (summary_only == 1)
{
if (json_out == 1)
printf("]}}");
return;
}
if (depths_only == 0)
{
if (json_out)
printf("],\n\"samples\": [\n");
char **col_vals = NULL, **col_names = NULL;
// printf("num_samples:%d\n",num_samples);
for (i = 0; i < num_samples; ++i)
{
uint32_t idx;
if (sample_ids != NULL)
idx = sample_ids[i];
else
idx = i;
// printf("ped_get_cols_info_by_id:%d \n",idx);
num_col_vals = ped_get_cols_info_by_id(ped_db_file_name,
&db,
NULL,
0,
idx,
&col_vals,
&col_names);
uint32_t j;
if (json_out == 1)
{
if (i > 0)
printf(",");
printf("{");
for (j = 0; j < num_col_vals; ++j)
{
if (j > 0)
printf(",");
printf("\"%s\":\"%s\"", col_names[j], col_vals[j]);
}
printf(",\"Pairend\":\"%u\",\"Split\":\"%u\"}\n",
sample_alt_depths[i].first,
sample_alt_depths[i].second);
}
else
{
if (i == 0)
{
for (j = 0; j < num_col_vals; ++j)
printf("%s\t", col_names[j]);
printf("Pairend\tSplit\n");
}
for (j = 0; j < num_col_vals; ++j)
printf("%s\t", col_vals[j]);
printf("%u\t%u\n",
sample_alt_depths[i].first,
sample_alt_depths[i].second);
}
}
}
if (json_out == 1)
printf("]}}");
sqlite3_close(db);
}
//}}}
//{{{void print_results_shard(struct giggle_index *gi,
void print_results_shard(
// struct giggle_index *gi_all[],
// char *ped_db_file_name,
Shard shard_array[],
struct stix_breakpoint *left,
struct stix_breakpoint *right,
uint32_t *sample_ids_all[],
char *filter,
struct uint_pair *sample_alt_depths_all[],
uint32_t num_samples_all[],
uint32_t size_num_samples_all,
char **agg_cols,
uint32_t num_agg_cols,
uint32_t json_out,
uint32_t summary_only,
uint32_t depths_only)
{
uint32_t i;
uint32_t num_col_vals;
int32_t zero_count, one_count;
uint32_t Q1, Q2, Q3, min, max;
int32_t counts[4];
// uint32_t size_num_samples_all = sizeof(num_samples_all) / sizeof(num_samples_all[0]);
// if(V_is_set ==1)
// fprintf(stderr,"<<<<<<<<<<num_samples_all[0]:%d\tnum_samples_all[1]:%d,",num_samples_all[0],num_samples_all[1]);
uint32_t ret = stix_get_summary_shard(sample_alt_depths_all,
sample_ids_all,
num_samples_all,
size_num_samples_all,
&zero_count,
&one_count,
&Q1,
&Q2,
&Q3,
&min,
&max,
counts);
if (json_out == 1)
printf("{ \"results\": {\n");
if (json_out == 1)
{
printf("\"summary\": [\n");
printf("{"
"\"name\":\"Total\", "
"\"zero_count\":\"%d\", "
"\"one_count\":\"%d\","
"\"quantiles\":[\"%u\",\"%u\",\"%u\"], "
"\"counts\":[\"%u\",\"%u\",\"%u\",\"%u\"]",
zero_count,
one_count,
Q1, Q2, Q3,
counts[0], counts[1], counts[2], counts[3]);
}
else
{
printf("Total\t0:1\t%d:%d\t%u:%u:%u\t%d:%d:%d:%d",
zero_count, one_count,
Q1, Q2, Q3,
counts[0], counts[1], counts[2], counts[3]);
}
if (depths_only == 1)
{
for (size_t num_sample_idx = 0; num_sample_idx < size_num_samples_all; num_sample_idx++)
{
uint32_t *sample_depths = NULL;
struct uint_pair *sample_alt_depths = sample_alt_depths_all[num_sample_idx];
ret = stix_get_sample_depths(sample_alt_depths, // todo! -> sharding
NULL,
num_samples_all[num_sample_idx],
&sample_depths);
if (json_out == 0)
{
for (i = 0; i < num_samples_all[num_sample_idx]; ++i)
printf("\t%d", sample_depths[i]);
}
else
{
printf(",\"depths_shard%ld\":[", num_sample_idx);
for (i = 0; i < num_samples_all[num_sample_idx]; ++i)
{
if (i != 0)
printf(",");
printf("%d", sample_depths[i]);
}
printf("]");
}
free(sample_depths);
}
}
if (json_out == 1)
printf("}");
printf("\n");
// sqlite3 *db = NULL;
/*---------------------*/
if (num_agg_cols > 0)
{
// printf(">>> %d",num_agg_cols);
for (size_t num_sample_idx = 0; num_sample_idx < size_num_samples_all; num_sample_idx++)
{
char ***uniq_vals;
uint32_t num_uniq_vals;
uint32_t **uniq_groups_ids;
uint32_t *uniq_groups_sizes;
sqlite3 *db = NULL;
num_uniq_vals = ped_get_uniq_col_groups(shard_array[num_sample_idx].stixdb_path,
&db,
agg_cols,
num_agg_cols,
filter,
&uniq_vals,
&uniq_groups_ids,
&uniq_groups_sizes);
for (i = 0; i < num_uniq_vals; ++i)
{
uint32_t j;
char *group_name_tmp, *group_name;
ret = asprintf(&group_name, "%s", uniq_vals[i][0]);
for (j = 1; j < num_agg_cols; ++j)
{
ret = asprintf(&group_name_tmp,
"%s,%s",
group_name,
uniq_vals[i][j]);
free(group_name);
group_name = group_name_tmp;
}
// fprintf(stderr,">>>>>>>>>>>>>>>>>>>%s",group_name);
ret = stix_get_summary(sample_alt_depths_all[num_sample_idx],
uniq_groups_ids[i],
uniq_groups_sizes[i],
&zero_count,
&one_count,
&Q1,
&Q2,
&Q3,
&min,
&max,
counts);
if (json_out)
{
printf(",{"
"\"name\":\"%s\", "
"\"zero_count\":\"%d\", "
"\"one_count\":\"%d\","
"\"quantiles\":[\"%u\",\"%u\",\"%u\"], "
"\"counts\":[\"%u\",\"%u\",\"%u\",\"%u\"]",
group_name,
zero_count,
one_count,
Q1, Q2, Q3,
counts[0], counts[1], counts[2], counts[3]);
}
else
{
printf("%s\t0:1\t%d:%d\t%u:%u:%u\t%d:%d:%d:%d",
group_name,
zero_count, one_count,
Q1, Q2, Q3,
counts[0], counts[1], counts[2], counts[3]);
}
if (depths_only == 1)
{
uint32_t *sample_depths = NULL;
ret = stix_get_sample_depths(sample_alt_depths_all[num_sample_idx],
uniq_groups_ids[i],
uniq_groups_sizes[i],
&sample_depths);
int k;
if (json_out == 0)
{
for (k = 0; k < uniq_groups_sizes[i]; ++k)
printf("\t%d", sample_depths[k]);
}
else
{
printf(",\"depths\":[");
for (k = 0; k < uniq_groups_sizes[i]; ++k)
{
if (k != 0)
printf(",");
printf("%d", sample_depths[k]);
}
printf("]");
}
free(sample_depths);
}
if (json_out == 1)
printf("}");
printf("\n");
free(group_name);
}
}
}
/*---------------------*/
if (summary_only == 1)
{
if (json_out == 1)
printf("]}}");
return;
}
if (depths_only == 0)
{
int current_line_no = 0;
for (size_t num_sample_idx = 0; num_sample_idx < size_num_samples_all; num_sample_idx++)
{
if (json_out)
printf("],\n\"samples_shard%ld\": [\n", num_sample_idx);
sqlite3 *db = NULL;
// printf("num_samples:%d\n",num_samples);
uint32_t num_samples = num_samples_all[num_sample_idx];
for (i = 0; i < num_samples; ++i)
{
uint32_t idx;
idx = i;
char **col_vals = NULL, **col_names = NULL;
// printf("ped_get_cols_info_by_id:%d,num_sample_idx:%ld \n",idx,num_sample_idx);
// printf("shard_array[num_sample_idx].stixdb_path:%s\n",shard_array[num_sample_idx].stixdb_path);
num_col_vals = ped_get_cols_info_by_id(shard_array[num_sample_idx].stixdb_path, // todo! -> sharding
&db,
NULL,
0,
idx,
&col_vals,
&col_names);
uint32_t j;
if (json_out == 1)
{
if (i > 0)
printf(",");
printf("{");
for (j = 0; j < num_col_vals; ++j)
{
if (j > 0)
printf(",");
printf("\"%s\":\"%s\"", col_names[j], col_vals[j]);
}
printf(",\"Pairend\":\"%u\",\"Split\":\"%u\"}\n",
sample_alt_depths_all[num_sample_idx][i].first,
sample_alt_depths_all[num_sample_idx][i].second);
// fflush(stdout);
}
else
{
if (num_sample_idx == 0 && i == 0) // only print header once
{
for (j = 0; j < num_col_vals; ++j)
printf("%s\t", col_names[j]);
printf("Pairend\tSplit\n");
}
// printf("%d\t",current_line_no);
// current_line_no ++;
for (j = 0; j < num_col_vals; ++j)
printf("%s\t", col_vals[j]);
printf("%u\t%u\n",
sample_alt_depths_all[num_sample_idx][i].first,
sample_alt_depths_all[num_sample_idx][i].second);
// fflush(stdout);
}
}
sqlite3_close(db);
fflush(stdout);
}
}
if (json_out == 1)
{
printf("]}}");
fflush(stdout);
}
// sqlite3_close(db);
}
//}}}
//{{{uint32_t parse_aggregate_csv(char *aggregate,
uint32_t parse_aggregate_csv(char *aggregate,
char ***agg_cols)
{
uint32_t i;
uint32_t num_agg_cols = 1;
for (i = 0; i < strlen(aggregate); ++i)
{
if (aggregate[i] == ',')
num_agg_cols += 1;
}
*agg_cols = (char **)malloc(num_agg_cols * sizeof(char *));
char *p = strtok(aggregate, ",");
uint32_t col_i = 0;
while (p != NULL)
{
(*agg_cols)[col_i] = p;
col_i += 1;
p = strtok(NULL, ",");
}
return num_agg_cols;
}
//}}}
//{{{void update_vcf_header(bcf_hdr_t *hdr)
void update_vcf_header(bcf_hdr_t *hdr,
uint32_t v_is_set,
char *sample_column)
{
char *STIX_QUANTS_LINE =
"##INFO=<ID=STIX_QUANTS,Number=3,Type=Integer,"
"Description=\"STIX quantile values.\">";
if (bcf_hdr_append(hdr, STIX_QUANTS_LINE) != 0)
errx(EX_DATAERR, "Error updating header\n");
char *STIX_QUANT_DEPTHS_LINE =
"##INFO=<ID=STIX_QUANT_DEPTHS,Number=4,Type=Integer,"
"Description=\"STIX quantile depths.\">";
if (bcf_hdr_append(hdr, STIX_QUANT_DEPTHS_LINE) != 0)
errx(EX_DATAERR, "Error updating header\n");
char *STIX_ZERO_LINE =
"##INFO=<ID=STIX_ZERO,Number=1,Type=Integer,"
"Description=\"STIX samples with zero evidence.\">";
if (bcf_hdr_append(hdr, STIX_ZERO_LINE) != 0)
errx(EX_DATAERR, "Error updating header\n");
char *STIX_ONE_LINE =
"##INFO=<ID=STIX_ONE,Number=1,Type=Integer,"
"Description=\"STIX samples with one piece of evidence.\">";
if (bcf_hdr_append(hdr, STIX_ONE_LINE) != 0)
errx(EX_DATAERR, "Error updating header\n");
char *MIN_SUP_READS_LINE =
"##INFO=<ID=STIX_ONE_MIN_READS,Number=1,Type=Integer,"
"Description=\"STIX How many supporting reads define a hit,Used for calucation of STIX_ONE and STIX_ZERO.\">";
if (bcf_hdr_append(hdr, MIN_SUP_READS_LINE) != 0)
errx(EX_DATAERR, "Error updating header\n");
if (v_is_set == 1)
{
char *STIX_SAMPLE_DEPTH_LINE =
"##INFO=<ID=STIX_SAMPLE_DEPTH,Number=.,Type=String,"
"Description=\"STIX sample-level depth information.\">";
if (bcf_hdr_append(hdr, STIX_SAMPLE_DEPTH_LINE) != 0)
errx(EX_DATAERR, "Error updating header\n");
}
}
//}}}
int V_is_set = 0; // init global Verbose mode
int L_is_set = 0; // init global Length of Insertions
int R_is_set = 0;
int T_is_set = 0;
uint32_t length_of_insertion = 0;
float ovpct_threshold = 0.15;
uint32_t min_supporting_reads = 1;
//{{{int main(int argc, char **argv)
int main(int argc, char **argv)
{
int c;
int i_is_set = 0,
s_is_set = 0,
p_is_set = 0,
c_is_set = 0,
d_is_set = 0,
r_is_set = 0,
l_is_set = 0,
f_is_set = 0,
a_is_set = 0,
F_is_set = 0,
j_is_set = 0,
t_is_set = 0,
v_is_set = 0,
P_is_set = 0,
Q_is_set = 0,
B_is_set = 0;
char *index_dir_name = NULL;
char *ped_file_name = NULL;
char *ped_db_file_name = NULL;
char *vcf_file_name = NULL;
char *r_region = NULL;
char *l_region = NULL;
char *aggregate = NULL;
char *filter = NULL;
char *sv_type = NULL;
char *sample_column = NULL;
char *sharding_file_name = NULL;
char *table_query_file_name = NULL;
uint32_t slop = 0;
uint32_t ins_padding = 50;
uint32_t col_id = 1;
uint32_t summary_only = 0;
uint32_t depths_only = 0;
while ((c = getopt(argc, argv, "i:P:s:T:B:Q:p:c:d:r:l:f:a:F:jt:v:SDVL:R:")) != -1)
{
switch (c)
{
case 'i':
i_is_set = 1;
index_dir_name = optarg;
break;
case 's':
s_is_set = 1;
slop = atoi(optarg);
break;
case 'B':
B_is_set = 1;
sharding_file_name = optarg;
break;
case 'Q':
Q_is_set = 1;
table_query_file_name = optarg;
break;
case 'p':
p_is_set = 1;
ped_file_name = optarg;
break;
case 'P':
P_is_set = 1;
ins_padding = atoi(optarg);
break;
case 'T':
T_is_set = 1;
min_supporting_reads = atoi(optarg);
break;
case 'c':
c_is_set = 1;
col_id = atoi(optarg);
break;
case 'd':
d_is_set = 1;
ped_db_file_name = optarg;
break;
case 'r':
r_is_set = 1;
r_region = optarg;
break;
case 'l':
l_is_set = 1;
l_region = optarg;
break;
case 'f':
f_is_set = 1;
vcf_file_name = optarg;
break;
case 'a':
a_is_set = 1;
aggregate = optarg;
break;
case 'F':
F_is_set = 1;
filter = optarg;
break;
case 'j':
j_is_set = 1;
break;
case 't':
t_is_set = 1;
sv_type = optarg;
break;
case 'L':
L_is_set = 1;
length_of_insertion = atoi(optarg);
break;
case 'R':
R_is_set = 1;
ovpct_threshold = atof(optarg);
break;
case 'v':
v_is_set = 1;
sample_column = optarg;
break;
case 'S':
summary_only = 1;
break;
case 'D':
depths_only = 1;
break;
case 'V':
V_is_set = 1;
break;
case 'h':
return help(EX_OK);
case '?':
if ((optopt == 'i') ||
(optopt == 's') ||
(optopt == 'B') ||
(optopt == 'Q') ||
(optopt == 'T') ||
(optopt == 'p') ||
(optopt == 'P') ||
(optopt == 'd') ||
(optopt == 'r') ||
(optopt == 'l') ||
(optopt == 'f') ||
(optopt == 'a') ||
(optopt == 'F') ||
(optopt == 't') ||
(optopt == 'L') ||
(optopt == 'R') ||
(optopt == 'v'))
fprintf(stderr,
"Option -%c requires an argument.\n",
optopt);
else if (isprint(optopt))
fprintf(stderr,
"Unknown option `-%c'.\n",
optopt);
else
fprintf(stderr,
"Unknown option character `\\x%x'.\n",
optopt);
return help(EX_USAGE);
default:
return help(EX_OK);
}
}
char **agg_cols = NULL;
uint32_t num_agg_cols = 0;
if (a_is_set == 1)
num_agg_cols = parse_aggregate_csv(aggregate, &agg_cols);
/*create index*/
if ((i_is_set == 1) &&
(p_is_set == 1) &&
(d_is_set == 1))
{
uint32_t num_rows = ped_create_db(ped_file_name,
ped_db_file_name,
index_dir_name,
col_id);
fprintf(stderr,
"PED database %s with %u rows created from %s.\n",
ped_db_file_name,
num_rows,
ped_file_name);
return EX_OK;
}
/*search*/
if (B_is_set == 0)
{ // single db mode
if ((i_is_set == 1) && // giggle index
(d_is_set == 1) && // ped db
(s_is_set == 1))
{ // slop
uint32_t *sample_ids = NULL;
uint32_t num_samples = 0;
if (F_is_set == 1)
num_samples = ped_get_matching_sample_ids(ped_db_file_name,
filter,
&sample_ids);
struct giggle_index *gi = NULL;
struct uint_pair *sample_alt_depths = NULL;
struct stix_breakpoint *left = NULL, *right = NULL;
/*Single query mode*/
if ((l_is_set == 1) && // left interval
(r_is_set == 1) && // right interval
(t_is_set == 1))
{ // sv type
left = stix_region_to_breakpoint(l_region);
right = stix_region_to_breakpoint(r_region);
enum stix_sv_type query_type = DEL;
if (strcmp(sv_type, "DUP") == 0)
query_type = DUP;
else if (strcmp(sv_type, "INV") == 0)
query_type = INV;
else if (strcmp(sv_type, "BND") == 0)
query_type = BND;
else if (strcmp(sv_type, "INS") == 0)
query_type = INS;
uint32_t num_sample_alt_depths =
stix_run_giggle_query(&gi,
index_dir_name,
query_type,
left,
right,
slop,
ins_padding,
sample_ids,
num_samples,
&sample_alt_depths,
0);
// DEBUG
// printf("num_sample_alt_depths:%d\n",num_sample_alt_depths);
print_results(gi,
ped_db_file_name,
left,
right,
sample_ids,
filter,
sample_alt_depths,
num_sample_alt_depths,
agg_cols,
num_agg_cols,
j_is_set,
summary_only,
depths_only);
free(left->chrm);
free(left);
free(right->chrm);
free(right);
}
else if (f_is_set == 1) /*VCF input mode*/
{
htsFile *fp = hts_open(vcf_file_name, "r");
if (!fp)
err(EX_DATAERR, "Could not read file: %s", vcf_file_name);
bcf_hdr_t *hdr = bcf_hdr_read(fp);
if (!hdr)
errx(EX_DATAERR, "Header not found: %s\n", vcf_file_name);
update_vcf_header(hdr, v_is_set, sample_column);
htsFile *out_f = hts_open("-", "w");
bcf_hdr_write(out_f, hdr);
bcf1_t *line = bcf_init1();