void vcf_hdrtxt_append_commands(cJSON *command, StrBuf *hdr, const char *path)
{
bool first;
for(; command != NULL; command = command->next)
{
cJSON *key = json_hdr_get(command, "key", cJSON_String, path);
cJSON *cmd = json_hdr_get(command, "cmd", cJSON_Array, path);
cJSON *cwd = json_hdr_get(command, "cwd", cJSON_String, path);
cJSON *prev = json_hdr_get(command, "prev", cJSON_Array, path);
cJSON *ver = json_hdr_try(command, "mccortex",cJSON_String, path);
prev = prev->child; // result could be NULL
if(prev && prev->type != cJSON_String) die("Invalid 'prev' field");
strbuf_append_str(hdr, "##mccortex_");
strbuf_append_str(hdr, key->valuestring);
strbuf_append_str(hdr, "=<prev=\"");
strbuf_append_str(hdr, prev ? prev->valuestring : "NULL");
if(prev) {
while((prev = prev->next) != NULL) {
strbuf_append_str(hdr, ";");
strbuf_append_str(hdr, prev->valuestring);
}
}
strbuf_append_str(hdr, "\",cmd=\"");
for(first = true, cmd = cmd->child; cmd; cmd = cmd->next, first = false) {
if(!first) strbuf_append_char(hdr, ' ');
strbuf_append_str(hdr, cmd->valuestring);
}
strbuf_append_str(hdr, "\",cwd=\"");
strbuf_append_str(hdr, cwd->valuestring);
strbuf_append_str(hdr, "\"");
if(ver) {
strbuf_append_str(hdr, ",version=\"");
strbuf_append_str(hdr, ver->valuestring);
strbuf_append_str(hdr, "\"");
}
strbuf_append_str(hdr, ">\n");
}
}
static void print_vcf_header(cJSON *json, bool is_breakpoint, FILE *fout)
{
ctx_assert(json != NULL);
char datestr[9];
time_t date = time(NULL);
strftime(datestr, 9, "%Y%m%d", localtime(&date));
fprintf(fout, "##fileformat=VCFv4.1\n##fileDate=%s\n", datestr);
// Print commands used to generate header
cJSON *commands = json_hdr_get(json, "commands", cJSON_Array, input_path);
cJSON *command = commands->child;
// Print this command
char keystr[8];
char *prevstr = NULL;
size_t i;
if(command) {
cJSON *key = json_hdr_get(command, "key", cJSON_String, input_path);
prevstr = key->valuestring;
}
// Print command entry for this command
fprintf(fout, "##mccortex_%s=<prev=\"%s\",cmd=\"%s\",cwd=\"%s\",version="CTX_VERSION">\n",
hex_rand_str(keystr, sizeof(keystr)),
prevstr ? prevstr : "NULL",
cmd_get_cmdline(), cmd_get_cwd());
// Print previous commands
for(; command != NULL; command = command->next)
{
cJSON *key = json_hdr_get(command, "key", cJSON_String, input_path);
cJSON *cmd = json_hdr_get(command, "cmd", cJSON_Array, input_path);
cJSON *cwd = json_hdr_get(command, "cwd", cJSON_String, input_path);
cJSON *prev = json_hdr_get(command, "prev", cJSON_Array, input_path);
cJSON *ver = json_hdr_try(command, "mccortex",cJSON_String, input_path);
prev = prev->child; // result could be NULL
if(prev && prev->type != cJSON_String) die("Invalid 'prev' field");
fprintf(fout, "##mccortex_%s=<prev=\"%s", key->valuestring,
prev ? prev->valuestring : "NULL");
if(prev) {
while((prev = prev->next) != NULL) fprintf(fout, ";%s", prev->valuestring);
}
fprintf(fout, "\",cmd=\"");
for(i = 0, cmd = cmd->child; cmd; cmd = cmd->next, i++) {
if(i > 0) fputc(' ', fout);
fputs(cmd->valuestring, fout);
}
fprintf(fout, "\",cwd=\"%s\"", cwd->valuestring);
if(ver) { fprintf(fout, ",version=\"%s\"", ver->valuestring); }
fprintf(fout, ">\n");
}
// Print field definitions
if(is_breakpoint)
fprintf(fout, "##INFO=<ID=BRKPNT,Number=1,Type=String,Description=\"Breakpoint call\">\n");
else
fprintf(fout, "##INFO=<ID=BUBBLE,Number=1,Type=String,Description=\"Bubble call\">\n");
fprintf(fout, "##INFO=<ID=K%zu,Number=0,Type=Flag,Description=\"Found at k=%zu\">\n", kmer_size, kmer_size);
fprintf(fout, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n");
fprintf(fout, "##FILTER=<ID=PASS,Description=\"All filters passed\">\n");
// Print reference paths
fprintf(fout, "##reference=%s", ref_paths[0]);
for(i = 1; i < num_ref_paths; i++) printf(",%s", ref_paths[i]);
fprintf(fout, "\n");
// Print contigs lengths
for(i = 0; i < chroms.len; i++) {
fprintf(fout, "##contig=<ID=%s,length=%zu>\n",
chroms.b[i].name.b, chroms.b[i].seq.end);
}
// Print VCF column header
fputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", fout);
if(is_breakpoint)
{
// Print a column for each sample
cJSON *graph_json = json_hdr_get(json, "graph", cJSON_Object, input_path);
cJSON *colours_json = json_hdr_get(graph_json, "colours", cJSON_Array, input_path);
cJSON *colour_json = colours_json->child;
if(colour_json == NULL) die("Missing colours");
for(; colour_json; colour_json = colour_json->next)
{
if(!json_hdr_colour_is_ref(colour_json)) {
cJSON *sample_json = json_hdr_get(colour_json, "sample", cJSON_String, input_path);
fputc('\t', fout);
fputs(sample_json->valuestring, fout);
}
}
}
fputc('\n', fout);
}
