int scconf_parse_entries(const scconf_context * config, const scconf_block * block, scconf_entry * entry)
{
if (!entry)
return 1;
if (!block)
block = config->root;
return parse_entries(config, block, entry, 0);
}
static gboolean
date_entry_focus_out (GtkWidget *widget,
GdkEvent *event,
gpointer user_data)
{
parse_entries (GCAL_DATE_SELECTOR (user_data));
return FALSE;
}
int parse_all(void const * start, void const * end,
unsigned long long end_time)
{
char const * ptr = start;
if (!parse_header(&ptr, end))
return parse_entries(ptr, end, end_time);
else
return OP_JIT_CONV_FAIL;
}
static int parse_type(const scconf_context * config, const scconf_block * block, scconf_entry * entry, int depth)
{
void *parm = entry->parm;
size_t *len = (size_t *) entry->arg;
int (*callback_func) (const scconf_context * config, const scconf_block * block, scconf_entry * entry, int depth) =
(int (*)(const scconf_context *, const scconf_block *, scconf_entry *, int)) parm;
int r = 0;
if (config->debug) {
fprintf(stderr, "decoding '%s'\n", entry->name);
}
switch (entry->type) {
case SCCONF_CALLBACK:
if (parm) {
r = callback_func(config, block, entry, depth);
}
break;
case SCCONF_BLOCK:
if (parm) {
r = parse_entries(config, block, (scconf_entry *) parm, depth + 1);
}
break;
case SCCONF_LIST:
{
const scconf_list *val = scconf_find_list(block, entry->name);
if (!val) {
r = 1;
break;
}
if (parm) {
if (entry->flags & SCCONF_ALLOC) {
scconf_list *dest = NULL;
for (; val != NULL; val = val->next) {
if (!scconf_list_add(&dest, val->data)) {
r = 1;
break;
}
}
*((scconf_list **) parm) = dest;
} else {
*((const scconf_list **) parm) = val;
}
}
if (entry->flags & SCCONF_VERBOSE) {
char *buf = scconf_list_strdup(val, ", ");
printf("%s = %s\n", entry->name, buf);
free(buf);
}
}
break;
case SCCONF_BOOLEAN:
{
int val = scconf_get_bool(block, entry->name, 0);
if (parm) {
*((int *) parm) = val;
}
if (entry->flags & SCCONF_VERBOSE) {
printf("%s = %s\n", entry->name, val == 0 ? "false" : "true");
}
}
break;
case SCCONF_INTEGER:
{
int val = scconf_get_int(block, entry->name, 0);
if (parm) {
*((int *) parm) = val;
}
if (entry->flags & SCCONF_VERBOSE) {
printf("%s = %i\n", entry->name, val);
}
}
break;
case SCCONF_STRING:
{
const char *val = scconf_get_str(block, entry->name, NULL);
int vallen = val ? strlen(val) : 0;
if (!vallen) {
r = 1;
break;
}
if (parm) {
if (entry->flags & SCCONF_ALLOC) {
char **buf = (char **) parm;
*buf = malloc(vallen + 1);
if (*buf == NULL) {
r = 1;
break;
}
memset(*buf, 0, vallen + 1);
if (len) {
*len = vallen;
}
parm = *buf;
}
memcpy((char *) parm, val, vallen);
}
if (entry->flags & SCCONF_VERBOSE) {
printf("%s = %s\n", entry->name, val);
}
}
break;
default:
fprintf(stderr, "invalid configuration type: %d\n", entry->type);
}
if (r) {
fprintf(stderr, "decoding of configuration entry '%s' failed.\n", entry->name);
return r;
}
entry->flags |= SCCONF_PRESENT;
return 0;
}
int ctx_calls2vcf(int argc, char **argv)
{
parse_cmdline_args(argc, argv);
size_t i;
// These functions call die() on error
gzFile gzin = futil_gzopen(input_path, "r");
nw_aligner_setup();
// Read file header
cJSON *json = read_input_header(gzin);
// Get format (bubble or breakpoint file)
cJSON *json_fmt = json_hdr_get(json, "file_format", cJSON_String, input_path);
if(strcmp(json_fmt->valuestring,"CtxBreakpoints") == 0) input_bubble_format = false;
else if(strcmp(json_fmt->valuestring,"CtxBubbles") == 0) input_bubble_format = true;
else die("Unknown format: '%s'", json_fmt->valuestring);
status("Reading %s in %s format", futil_inpath_str(input_path),
input_bubble_format ? "bubble" : "breakpoint");
if(input_bubble_format && sam_path == NULL)
cmd_print_usage("Require -F <flanks.sam> with bubble file");
// Open flank file if it exists
if(sam_path) flanks_sam_open();
// Open output file
FILE *fout = futil_fopen_create(out_path, "w");
// Load reference genome
read_buf_alloc(&chroms, 1024);
genome = kh_init(ChromHash);
seq_reader_load_ref_genome(ref_paths, num_ref_paths, &chroms, genome);
// convert to upper case
char *s;
for(i = 0; i < chroms.len; i++)
for(s = chroms.b[i].seq.b; *s; s++) *s = toupper(*s);
if(!input_bubble_format) brkpnt_check_refs_match(json, input_path);
// Output VCF has 0 samples if bubbles file, otherwise has N where N is
// number of samples/colours in the breakpoint graph
size_t num_graph_samples = json_hdr_get_ncols(json, input_path);
size_t num_graph_nonref = json_hdr_get_nonref_ncols(json, input_path);
num_samples = 0;
if(!input_bubble_format) {
// If last colour has "is_ref", drop number of samples by one
num_samples = num_graph_nonref < num_graph_samples ? num_graph_samples-1
: num_graph_samples;
}
print_vcf_header(json, !input_bubble_format, fout);
status("Reading %s call file with %zu samples",
input_bubble_format ? "Bubble" : "Breakpoint", num_graph_samples);
status("Writing a VCF with %zu samples", num_samples);
parse_entries(gzin, fout);
// Print stats
char num_entries_read_str[50];
char num_vars_printed_str[50];
ulong_to_str(num_entries_read, num_entries_read_str);
ulong_to_str(num_vars_printed, num_vars_printed_str);
status("Read %s entries, printed %s vcf entries to: %s",
num_entries_read_str, num_vars_printed_str, futil_outpath_str(out_path));
if(input_bubble_format) {
char msg[200];
// Bubble caller specific
print_stat(num_flank5p_unmapped, num_entries_read, "flank 5p unmapped");
sprintf(msg, "flank 5p low mapq (<%zu)", min_mapq);
print_stat(num_flank5p_lowqual, num_entries_read, msg);
print_stat(num_flank3p_not_found, num_entries_read, "flank 3p not found");
print_stat(num_flank3p_multihits, num_entries_read, "flank 3p multiple hits");
print_stat(num_flank3p_approx_match,num_entries_read, "flank 3p approx match used");
print_stat(num_flank3p_exact_match, num_entries_read, "flank 3p exact match");
} else {
// Breakpoint caller specific
print_stat(num_flanks_not_uniquely_mapped, num_entries_read, "flank pairs contain one flank not mapped uniquely");
print_stat(num_flanks_diff_chroms, num_entries_read, "flank pairs map to diff chroms");
print_stat(num_flanks_diff_strands, num_entries_read, "flank pairs map to diff strands");
}
print_stat(num_flanks_too_far_apart, num_entries_read, "flank pairs too far apart");
print_stat(num_flanks_overlap_too_large, num_entries_read, "flank pairs overlap too much");
print_stat(num_entries_well_mapped, num_entries_read, "flank pairs map well");
status("Aligned %zu allele pairs and %zu flanks", num_nw_allele, num_nw_flank);
// Finished - clean up
cJSON_Delete(json);
gzclose(gzin);
fclose(fout);
for(i = 0; i < chroms.len; i++) seq_read_dealloc(&chroms.b[i]);
read_buf_dealloc(&chroms);
kh_destroy_ChromHash(genome);
nw_aligner_destroy();
if(sam_path) flanks_sam_close();
// hide unused method warnings
(void)kh_del_ChromHash;
(void)kh_put_ChromHash;
(void)kh_get_ChromHash;
(void)kh_clear_ChromHash;
(void)kh_destroy_ChromHash;
(void)kh_init_ChromHash;
return EXIT_SUCCESS;
}
static void
entry_activated (GtkEntry *entry,
gpointer user_data)
{
parse_entries (GCAL_DATE_SELECTOR (user_data));
}
