// Check contig entries match reference
// We check that these match the reference just loaded
static void brkpnt_check_refs_match(cJSON *json,
const ChromHash *genome,
const char *path)
{
cJSON *version = json_hdr_get(json, "format_version", cJSON_Number, path);
if(version->valueint <= 2) return;
cJSON *command = json_hdr_get_curr_cmd(json, path);
cJSON *brkpnts = json_hdr_get(command, "breakpoints", cJSON_Object, path);
cJSON *contigs = json_hdr_get(brkpnts, "contigs", cJSON_Array, path);
cJSON *contig;
size_t num_chroms = 0;
for(contig = contigs->child; contig; contig = contig->next, num_chroms++)
{
cJSON *id = json_hdr_get(contig, "id", cJSON_String, path);
cJSON *len = json_hdr_get(contig, "length", cJSON_Number, path);
// Check chrom is loaded in ref and of expected length
khiter_t k = kh_get(kChromHash, genome, id->valuestring);
if(k == kh_end(genome)) warn("Cannot find chrom [%s]", id->valuestring);
else {
const read_t *r = kh_value(genome, k);
if(r->seq.end != (size_t)len->valueint) {
warn("Chrom lengths do not match %s input:%li ref:%zu",
id->valuestring, len->valueint, r->seq.end);
}
}
}
if(num_chroms != kh_size(genome)) {
warn("Number of chromosomes differ: %zu in header vs %zu in ref",
num_chroms, (size_t)kh_size(genome));
}
}
/**
* Generate a JSON header object for a .ctp file
* @param path path to output file
* @param cmdstr name of the command being run, to be used to add @cmdhdr
* @param cmdhdr JSON header to add under current command->@cmdstr
* If cmdstr and cmdhdr are both NULL they are ignored
* @param contig_hist histgram of read contig lengths
* @param hist_len length of array contig_hist
*/
cJSON* gpath_save_mkhdr(const char *path,
const char *cmdstr, cJSON *cmdhdr,
cJSON **hdrs, size_t nhdrs,
const ZeroSizeBuffer *contig_hists, size_t ncols,
const dBGraph *db_graph)
{
ctx_assert(!cmdstr == !cmdhdr);
const GPathStore *gpstore = &db_graph->gpstore;
const GPathSet *gpset = &gpstore->gpset;
// using json_hdr_make_std() assumes the following
ctx_assert(gpset->ncols == db_graph->num_of_cols);
// Construct cJSON
cJSON *jsonhdr = cJSON_CreateObject();
cJSON_AddStringToObject(jsonhdr, "file_format", "ctp");
cJSON_AddNumberToObject(jsonhdr, "format_version", CTP_FORMAT_VERSION);
// Add standard cortex header info, including the command being run
json_hdr_make_std(jsonhdr, path, hdrs, nhdrs, db_graph,
hash_table_nkmers(&db_graph->ht));
// Get first command (this one), and command specific extra info
if(cmdstr) {
cJSON *cmd = json_hdr_get_curr_cmd(jsonhdr, path);
cJSON_AddItemToObject(cmd, cmdstr, cmdhdr);
}
// Paths info
cJSON *paths = cJSON_CreateObject();
cJSON_AddItemToObject(jsonhdr, "paths", paths);
// Add command specific header fields
cJSON_AddNumberToObject(paths, "num_kmers_with_paths", gpstore->num_kmers_with_paths);
cJSON_AddNumberToObject(paths, "num_paths", gpstore->num_paths);
cJSON_AddNumberToObject(paths, "path_bytes", gpstore->path_bytes);
// Add size distribution
cJSON *json_hists = cJSON_CreateArray();
cJSON_AddItemToObject(paths, "contig_hists", json_hists);
size_t i;
for(i = 0; i < ncols; i++)
_gpath_save_contig_hist2json(json_hists, contig_hists[i].b, contig_hists[i].len);
return jsonhdr;
}
// Check contig entries match reference
// We check that these match the reference just loaded
static void brkpnt_check_refs_match(cJSON *json, const char *path)
{
cJSON *version = json_hdr_get(json, "format_version", cJSON_Number, path);
if(version->valueint <= 2) return;
cJSON *command = json_hdr_get_curr_cmd(json, path);
cJSON *brkpnts = json_hdr_get(command, "breakpoints", cJSON_Object, path);
cJSON *contigs = json_hdr_get(brkpnts, "contigs", cJSON_Array, path);
cJSON *contig;
size_t num_chroms = 0;
for(contig = contigs->child; contig; contig = contig->next, num_chroms++)
{
cJSON *id = json_hdr_get(contig, "id", cJSON_String, path);
cJSON *len = json_hdr_get(contig, "length", cJSON_Number, path);
const char *chrom_name = id->valuestring;
long chrom_len = len->valueint;
size_t reflen;
khiter_t k = kh_get(ChromHash, genome, chrom_name);
if(k == kh_end(genome))
die("Cannot find ref chrom: %s", chrom_name);
else {
reflen = kh_value(genome, k)->seq.end;
if(reflen != (size_t)chrom_len) {
die("Chrom lengths do not match %s input:%li ref:%zu",
chrom_name, chrom_len, reflen);
}
}
}
if(num_chroms != chroms.len) {
die("Number of chromosomes differ: %zu in header vs %zu in ref",
num_chroms, chroms.len);
}
}
