int bcf_hdr_set(bcf_hdr_t *hdr, const char *fname)
{
int i, n;
char **lines = hts_readlines(fname, &n);
if ( !lines ) return 1;
for (i=0; i<n-1; i++)
{
int k;
bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr,lines[i],&k);
bcf_hdr_add_hrec(hdr, hrec);
free(lines[i]);
}
bcf_hdr_parse_sample_line(hdr,lines[n-1]);
free(lines[n-1]);
free(lines);
bcf_hdr_sync(hdr);
bcf_hdr_fmt_text(hdr);
return 0;
}
static void reheader_bcf(args_t *args, int is_compressed)
{
htsFile *fp = hts_open(args->fname, "r"); if ( !fp ) error("Failed to open: %s\n", args->fname);
bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to read the header: %s\n", args->fname);
kstring_t htxt = {0,0,0};
int hlen;
htxt.s = bcf_hdr_fmt_text(hdr, 1, &hlen);
htxt.l = hlen;
int i, nsamples = 0;
char **samples = NULL;
if ( args->samples_fname )
samples = hts_readlines(args->samples_fname, &nsamples);
if ( args->header_fname )
{
free(htxt.s); htxt.s = NULL; htxt.l = htxt.m = 0;
read_header_file(args->header_fname, &htxt);
}
if ( samples )
{
set_samples(samples, nsamples, &htxt);
for (i=0; i<nsamples; i++) free(samples[i]);
free(samples);
}
bcf_hdr_t *hdr_out = bcf_hdr_init("r");
bcf_hdr_parse(hdr_out, htxt.s);
if ( args->header_fname ) hdr_out = strip_header(hdr, hdr_out);
// write the header and the body
htsFile *fp_out = hts_open("-",is_compressed ? "wb" : "wbu");
bcf_hdr_write(fp_out, hdr_out);
bcf1_t *rec = bcf_init();
while ( bcf_read(fp, hdr, rec)==0 )
{
// sanity checking, this slows things down. Make it optional?
bcf_unpack(rec, BCF_UN_ALL);
if ( rec->rid >= hdr_out->n[BCF_DT_CTG] || strcmp(bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid),bcf_hdr_int2id(hdr_out,BCF_DT_CTG,rec->rid)) )
error("The CHROM is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid));
for (i=0; i<rec->d.n_flt; i++)
{
int id = rec->d.flt[i];
if ( id >= hdr_out->n[BCF_DT_ID] ) break;
if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FLT,id) ) break;
if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
error("FIXME: Broken FILTER ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
}
if ( i!=rec->d.n_flt )
error("The FILTER is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i]));
for (i=0; i<rec->n_info; i++)
{
int id = rec->d.info[i].key;
if ( id >= hdr_out->n[BCF_DT_ID] ) break;
if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_INFO,id) ) break;
if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
error("FIXME: Broken INFO ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
}
if ( i!=rec->n_info )
error("The INFO tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.info[i].key));
for (i=0; i<rec->n_fmt; i++)
{
int id = rec->d.fmt[i].id;
if ( id >= hdr_out->n[BCF_DT_ID] ) break;
if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break;
if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
error("FIXME: Broken FORMAT ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
}
if ( i!=rec->n_fmt )
error("The FORMAT tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.fmt[i].id));
bcf_write(fp_out,hdr_out,rec);
}
bcf_destroy(rec);
free(htxt.s);
hts_close(fp_out);
hts_close(fp);
bcf_hdr_destroy(hdr_out);
bcf_hdr_destroy(hdr);
}
bcf_hdr_t *vcf_hdr_read(htsFile *fp)
{
if (!fp->is_bin) {
kstring_t txt, *s = &fp->line;
bcf_hdr_t *h;
h = bcf_hdr_init();
txt.l = txt.m = 0; txt.s = 0;
while (hts_getline(fp, KS_SEP_LINE, s) >= 0) {
if (s->l == 0) continue;
if (s->s[0] != '#') {
if (hts_verbose >= 2)
fprintf(stderr, "[E::%s] no sample line\n", __func__);
free(txt.s);
bcf_hdr_destroy(h);
return 0;
}
if (s->s[1] != '#' && fp->fn_aux) { // insert contigs here
int dret;
gzFile f;
kstream_t *ks;
kstring_t tmp;
tmp.l = tmp.m = 0; tmp.s = 0;
f = gzopen(fp->fn_aux, "r");
ks = ks_init(f);
while (ks_getuntil(ks, 0, &tmp, &dret) >= 0) {
int c;
kputs("##contig=<ID=", &txt); kputs(tmp.s, &txt);
ks_getuntil(ks, 0, &tmp, &dret);
kputs(",length=", &txt); kputw(atol(tmp.s), &txt);
kputsn(">\n", 2, &txt);
if (dret != '\n')
while ((c = ks_getc(ks)) != '\n' && c != -1); // skip the rest of the line
}
free(tmp.s);
ks_destroy(ks);
gzclose(f);
}
kputsn(s->s, s->l, &txt);
if (s->s[1] != '#') break;
kputc('\n', &txt);
}
h->l_text = txt.l + 1; // including NULL
h->text = txt.s;
bcf_hdr_parse(h);
// check tabix index, are all contigs listed in the header? add the missing ones
tbx_t *idx = tbx_index_load(fp->fn);
if ( idx )
{
int i, n, need_sync = 0;
const char **names = tbx_seqnames(idx, &n);
for (i=0; i<n; i++)
{
bcf_hrec_t *hrec = bcf_hdr_get_hrec(h, BCF_DT_CTG, (char*) names[i]);
if ( hrec ) continue;
hrec = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
hrec->key = strdup("contig");
bcf_hrec_add_key(hrec, "ID", strlen("ID"));
bcf_hrec_set_val(hrec, hrec->nkeys-1, (char*) names[i], strlen(names[i]), 0);
bcf_hrec_add_key(hrec, "length", strlen("length"));
bcf_hrec_set_val(hrec, hrec->nkeys-1, "-1", strlen("-1"), 0); // what is a good default value?
bcf_hdr_add_hrec(h, hrec);
need_sync = 1;
}
free(names);
tbx_destroy(idx);
if ( need_sync )
{
bcf_hdr_sync(h);
bcf_hdr_fmt_text(h);
}
}
return h;
} else return bcf_hdr_read((BGZF*)fp->fp);
}
void isec_vcf(args_t *args)
{
bcf_srs_t *files = args->files;
kstring_t str = {0,0,0};
htsFile *out_fh = NULL;
// When only one VCF is output, print VCF to stdout
int out_std = 0;
if ( args->nwrite==1 ) out_std = 1;
if ( args->targets_fname && files->nreaders==1 ) out_std = 1;
if ( out_std )
{
out_fh = hts_open("-",hts_bcf_wmode(args->output_type));
bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
bcf_hdr_fmt_text(files->readers[args->iwrite].header);
bcf_hdr_write(out_fh, files->readers[args->iwrite].header);
}
int n;
while ( (n=bcf_sr_next_line(files)) )
{
bcf_sr_t *reader = NULL;
bcf1_t *line = NULL;
int i, ret = 0;
for (i=0; i<files->nreaders; i++)
{
if ( !bcf_sr_has_line(files,i) ) continue;
if ( !line )
{
line = files->readers[i].buffer[0];
reader = &files->readers[i];
}
ret |= 1<<i; // this may overflow for many files, but will be used only with two (OP_VENN)
}
switch (args->isec_op)
{
case OP_COMPLEMENT: if ( n!=1 || !bcf_sr_has_line(files,0) ) continue; break;
case OP_EQUAL: if ( n != args->isec_n ) continue; break;
case OP_PLUS: if ( n < args->isec_n ) continue; break;
case OP_MINUS: if ( n > args->isec_n ) continue;
}
if ( out_std )
{
bcf_write1(out_fh, files->readers[args->iwrite].header, files->readers[args->iwrite].buffer[0]);
continue;
}
else if ( args->fh_sites )
{
str.l = 0;
kputs(reader->header->id[BCF_DT_CTG][line->rid].key, &str); kputc('\t', &str);
kputw(line->pos+1, &str); kputc('\t', &str);
if (line->n_allele > 0) kputs(line->d.allele[0], &str);
else kputc('.', &str);
kputc('\t', &str);
if (line->n_allele > 1) kputs(line->d.allele[1], &str);
else kputc('.', &str);
for (i=2; i<line->n_allele; i++)
{
kputc(',', &str);
kputs(line->d.allele[i], &str);
}
kputc('\t', &str);
for (i=0; i<files->nreaders; i++)
kputc(bcf_sr_has_line(files,i)?'1':'0', &str);
kputc('\n', &str);
fwrite(str.s,sizeof(char),str.l,args->fh_sites);
}
if ( args->prefix )
{
if ( args->isec_op==OP_VENN )
bcf_write1(args->fh_out[ret-1], reader->header, line);
else
{
for (i=0; i<files->nreaders; i++)
{
if ( !bcf_sr_has_line(files,i) ) continue;
if ( args->write && !args->write[i] ) continue;
bcf_write1(args->fh_out[i], files->readers[i].header, files->readers[i].buffer[0]);
}
}
}
}
if ( str.s ) free(str.s);
if ( out_fh ) hts_close(out_fh);
}
