static bcf_hdr_t* make_vcf_hdr(cJSON *json, const char *in_path,
bool is_breakpoint, size_t kmer_size,
char const*const* ref_paths, size_t nref_paths,
read_t *chroms, size_t nchroms)
{
ctx_assert(json != NULL);
StrBuf hdrbuf;
strbuf_alloc(&hdrbuf, 1024);
char datestr[9];
time_t date = time(NULL);
strftime(datestr, 9, "%Y%m%d", localtime(&date));
strbuf_append_str(&hdrbuf, "##fileformat=VCFv4.2\n##fileDate=");
strbuf_append_str(&hdrbuf, datestr);
strbuf_append_str(&hdrbuf, "\n");
// Print commands used to generate header
cJSON *commands = json_hdr_get(json, "commands", cJSON_Array, in_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, in_path);
prevstr = key->valuestring;
}
// Print command entry for this command
strbuf_append_str(&hdrbuf, "##mccortex_");
strbuf_append_str(&hdrbuf, hex_rand_str(keystr, sizeof(keystr)));
strbuf_append_str(&hdrbuf, "=<prev=\"");
strbuf_append_str(&hdrbuf, prevstr ? prevstr : "NULL");
strbuf_append_str(&hdrbuf, "\",cmd=\"");
strbuf_append_str(&hdrbuf, cmd_get_cmdline());
strbuf_append_str(&hdrbuf, "\",cwd=\"");
strbuf_append_str(&hdrbuf, cmd_get_cwd());
strbuf_append_str(&hdrbuf, "\",version="CTX_VERSION">\n");
// Print previous commands
vcf_hdrtxt_append_commands(command, &hdrbuf, in_path);
// Print field definitions
if(is_breakpoint)
strbuf_append_str(&hdrbuf, "##INFO=<ID=BRKPNT,Number=1,Type=String,Description=\"Breakpoint call\">\n");
else
strbuf_append_str(&hdrbuf, "##INFO=<ID=BUBBLE,Number=1,Type=String,Description=\"Bubble call\">\n");
strbuf_sprintf(&hdrbuf, "##INFO=<ID=K%zu,Number=0,Type=Flag,Description=\"Found at k=%zu\">\n", kmer_size, kmer_size);
strbuf_append_str(&hdrbuf, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n");
strbuf_append_str(&hdrbuf, "##FILTER=<ID=PASS,Description=\"All filters passed\">\n");
// Print reference paths
strbuf_append_str(&hdrbuf, "##reference=");
strbuf_append_str(&hdrbuf, ref_paths[0]);
for(i = 1; i < nref_paths; i++) {
strbuf_append_char(&hdrbuf, ',');
strbuf_append_str(&hdrbuf, ref_paths[i]);
}
strbuf_append_str(&hdrbuf, "\n");
// Print contigs lengths
for(i = 0; i < nchroms; i++) {
strbuf_sprintf(&hdrbuf, "##contig=<ID=%s,length=%zu>\n",
chroms[i].name.b, chroms[i].seq.end);
}
// Print VCF column header
strbuf_append_str(&hdrbuf, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
if(is_breakpoint)
{
// Print a column for each sample
cJSON *graph_json = json_hdr_get(json, "graph", cJSON_Object, in_path);
cJSON *colours_json = json_hdr_get(graph_json, "colours", cJSON_Array, in_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, in_path);
strbuf_append_str(&hdrbuf, "\t");
strbuf_append_str(&hdrbuf, sample_json->valuestring);
}
}
}
strbuf_append_char(&hdrbuf, '\n');
bcf_hdr_t *hdr = bcf_hdr_init("w");
if(bcf_hdr_parse(hdr, hdrbuf.b) != 0) die("Cannot construct VCF header");
strbuf_dealloc(&hdrbuf);
return hdr;
}
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);
}
