/**
* 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;
}
// Print JSON header to gzout
static void bubble_caller_print_header(gzFile gzout, const char* out_path,
BubbleCallingPrefs prefs,
cJSON **hdrs, size_t nhdrs,
const dBGraph *db_graph)
{
size_t i;
// Construct cJSON
cJSON *json = cJSON_CreateObject();
cJSON_AddStringToObject(json, "file_format", "CtxBubbles");
cJSON_AddNumberToObject(json, "format_version", BUBBLE_FORMAT_VERSION);
// Add standard cortex headers
json_hdr_make_std(json, out_path, hdrs, nhdrs, db_graph);
// Add parameters used in bubble calling to the header
json_hdr_augment_cmd(json, "bubbles", "max_flank_kmers", cJSON_CreateInt(prefs.max_flank_len));
json_hdr_augment_cmd(json, "bubbles", "max_allele_kmers", cJSON_CreateInt(prefs.max_allele_len));
cJSON *haploids = cJSON_CreateArray();
for(i = 0; i < prefs.num_haploid; i++)
cJSON_AddItemToArray(haploids, cJSON_CreateInt(prefs.haploid_cols[i]));
json_hdr_augment_cmd(json, "bubbles", "haploid_colours", haploids);
// Write header to file
json_hdr_gzprint(json, gzout);
// Print comments about the format
gzputs(gzout, "\n");
gzputs(gzout, "# This file was generated with McCortex\n");
gzputs(gzout, "# written by Isaac Turner <*****@*****.**>\n");
gzputs(gzout, "# url: "CORTEX_URL"\n");
gzputs(gzout, "# \n");
gzputs(gzout, "# Comment lines begin with a # and are ignored, but must come after the header\n");
gzputs(gzout, "\n");
cJSON_Delete(json);
}