/**
* Initialize next interval.
* Returns false only if all intervals are accessed.
*/
bool BCFOrderedReader::initialize_next_interval()
{
while (interval_index!=intervals.size())
{
if (ftype.format==bcf)
{
intervals[interval_index++].to_string(&s);
itr = bcf_itr_querys(idx, hdr, s.s);
if (itr)
{
return true;
}
}
else if (ftype.format==vcf && ftype.compression==bgzf)
{
intervals[interval_index++].to_string(&s);
itr = tbx_itr_querys(tbx, s.s);
if (itr)
{
return true;
}
}
}
return false;
};
/**
* Jump to interval. Returns false if not successful.
*
* @interval - string representation of interval.
*/
bool BCFOrderedReader::jump_to_interval(GenomeInterval& interval)
{
if (index_loaded)
{
intervals_present = true;
random_access_enabled = true;
intervals.clear();
intervals.push_back(interval);
interval_index = 0;
if (ftype.format==bcf)
{
intervals[interval_index++].to_string(&s);
itr = bcf_itr_querys(idx, hdr, s.s);
if (itr)
{
return true;
}
}
else if (ftype.format==vcf && ftype.compression==bgzf)
{
intervals[interval_index++].to_string(&s);
itr = tbx_itr_querys(tbx, s.s);
if (itr)
{
return true;
}
}
}
return false;
};
/**
* @brief pre-fetches the next variant record
* @warning we're reusing the existing htslib memory, so users should be aware that all objects from the previous iteration are now stale unless a deep copy has been performed
*/
void IndexedVariantIterator::fetch_next_record() {
while (bcf_itr_next(m_variant_file_ptr, m_index_iter_ptr.get(), m_variant_record_ptr.get()) < 0) {
++m_interval_iter;
if (m_interval_list.end() == m_interval_iter) {
m_variant_file_ptr.reset();
m_variant_record = Variant{};
return;
}
m_index_iter_ptr.reset(bcf_itr_querys(m_variant_index_ptr.get(), m_variant_header_ptr.get(), m_interval_iter->c_str()));
}
}
IndexedVariantIterator::IndexedVariantIterator(const std::shared_ptr<htsFile>& file_ptr,
const std::shared_ptr<hts_idx_t>& index_ptr,
const std::shared_ptr<bcf_hdr_t>& header_ptr,
const std::vector<std::string> interval_list) :
VariantIterator { file_ptr, header_ptr },
m_variant_index_ptr { index_ptr },
m_interval_list { interval_list.empty() ? all_intervals : move(interval_list) },
m_interval_iter { m_interval_list.begin() },
m_index_iter_ptr { utils::make_unique_hts_itr(bcf_itr_querys(m_variant_index_ptr.get(), m_variant_header_ptr.get(), m_interval_iter->c_str())) }
{
fetch_next_record();
}
/**
* Initialize buffer for next interval.
* This should only be invoked if the buffer is empty.
* Returns true if successful.
*/
bool BCFSyncedReader::initialize_next_interval()
{
if (random_access)
{
while (intervals_index < intervals.size())
{
GenomeInterval interval = intervals[intervals_index++];
for (size_t i=0; i<nfiles; ++i)
{
hts_itr_destroy(itrs[i]);
itrs[i] = 0;
interval.to_string(&s);
if (ftypes[i].format==bcf)
{
itrs[i] = bcf_itr_querys(idxs[i], hdrs[i], s.s);
}
else if (ftypes[i].format==vcf)
{
itrs[i] = tbx_itr_querys(tbxs[i], s.s);
}
fill_buffer(i);
}
//make sure pq is not empty
//it is possible for the pq to be empty as iterators may be returned
//as the sequence might be a valid sequence stated in the header
if (pq.size()!=0)
{
return true;
}
}
return false;
}
else
{
for (size_t i=0; i<nfiles; ++i)
{
fill_buffer(i);
}
if (pq.size()!=0)
{
return true;
}
return false;
}
}
/**
* Initialize buffer for next interval.
* This should only be invoked if the buffer is empty.
* Returns true if successful.
*/
bool BCFSyncedStreamReader::initialize_next_interval()
{
while (intervals_index < intervals.size())
{
GenomeInterval interval = intervals[intervals_index++];
for (int32_t i = 0; i<nfiles; ++i)
{
int32_t ftype = hts_file_type(vcf_files[i].c_str());
hts_itr_destroy(itrs[i]);
itrs[i] = 0;
interval.to_string(&s);
if (ftype==FT_BCF_GZ)
{
itrs[i] = bcf_itr_querys(idxs[i], hdrs[i], s.s);
}
else if (ftype==FT_VCF_GZ)
{
itrs[i] = tbx_itr_querys(tbxs[i], s.s);
}
fill_buffer(i);
}
//make sure pq is not empty
//it is possible for the pq to be empty as iterators may be returned
//as the sequence might be a valid sequence stated in the header
if (pq.size()!=0)
{
return true;
}
}
return false;
}
int main_vcfview(int argc, char *argv[])
{
int i, c, clevel = -1, flag = 0, n_samples = -1, *imap = 0, excl_snp = 0, excl_indel = 0;
char *fn_ref = 0, *fn_out = 0, moder[8], **samples = 0;
bcf_hdr_t *h, *hsub = 0;
htsFile *in;
bcf1_t *b;
while ((c = getopt(argc, argv, "l:bSt:o:T:s:GNI")) >= 0) {
switch (c) {
case 'l': clevel = atoi(optarg); flag |= 2; break;
case 'S': flag |= 1; break;
case 'b': flag |= 2; break;
case 'G': n_samples = 0; break;
case 't': fn_ref = optarg; flag |= 1; break;
case 'o': fn_out = optarg; break;
case 's': samples = hts_readlines(optarg, &n_samples); break;
case 'N': excl_snp = 1; break;
case 'I': excl_indel = 1; break;
}
}
if (argc == optind) {
fprintf(stderr, "\nUsage: vcfview [options] <in.bcf>|<in.vcf>|<in.vcf.gz>\n\n");
fprintf(stderr, "Options: -b output in BCF\n");
fprintf(stderr, " -S input is VCF\n");
fprintf(stderr, " -o FILE output file name [stdout]\n");
fprintf(stderr, " -l INT compression level [%d]\n", clevel);
fprintf(stderr, " -t FILE list of reference names and lengths [null]\n");
fprintf(stderr, " -s FILE/STR list of samples (STR if started with ':'; FILE otherwise) [null]\n");
fprintf(stderr, " -G drop individual genotype information\n");
fprintf(stderr, " -N exclude SNPs\n");
fprintf(stderr, " -I exclude INDELs\n");
fprintf(stderr, "\n");
return 1;
}
strcpy(moder, "r");
if ((flag&1) == 0 && !(file_type(argv[optind])&(IS_VCF|IS_VCF_GZ))) strcat(moder, "b");
in = hts_open(argv[optind], moder, fn_ref);
h = vcf_hdr_read(in);
if (h == 0) {
fprintf(stderr, "[E::%s] fail to read the VCF/BCF2 header\n", __func__);
hts_close(in);
return 1;
}
if (n_samples >= 0) {
if (n_samples) imap = (int*)malloc(n_samples * sizeof(int));
hsub = bcf_hdr_subset(h, n_samples, samples, imap);
}
b = bcf_init1();
if ((flag&4) == 0) { // VCF/BCF output
htsFile *out;
char modew[8];
strcpy(modew, "w");
if (clevel >= 0 && clevel <= 9) sprintf(modew + 1, "%d", clevel);
if (flag&2) strcat(modew, "b");
out = hts_open(fn_out? fn_out : "-", modew, 0);
vcf_hdr_write(out, hsub? hsub : h);
if (optind + 1 < argc && !(flag&1)) { // BAM input and has a region
hts_idx_t *idx;
if ((idx = bcf_index_load(argv[optind])) == 0) {
fprintf(stderr, "[E::%s] fail to load the BCF index\n", __func__);
return 1;
}
for (i = optind + 1; i < argc; ++i) {
hts_itr_t *iter;
if ((iter = bcf_itr_querys(idx, h, argv[i])) == 0) {
fprintf(stderr, "[E::%s] fail to parse region '%s'\n", __func__, argv[i]);
continue;
}
while (bcf_itr_next((BGZF*)in->fp, iter, b) >= 0) {
if (excl_snp && bcf_is_snp(b)) continue;
if (excl_indel && !bcf_is_snp(b)) continue;
if (n_samples >= 0) {
bcf_subset(h, b, n_samples, imap);
vcf_write1(out, hsub, b);
} else vcf_write1(out, h, b);
}
hts_itr_destroy(iter);
}
hts_idx_destroy(idx);
} else {
while (vcf_read1(in, h, b) >= 0) {
if (excl_snp && bcf_is_snp(b)) continue;
if (excl_indel && !bcf_is_snp(b)) continue;
if (n_samples >= 0) {
bcf_subset(h, b, n_samples, imap);
vcf_write1(out, hsub, b);
} else vcf_write1(out, h, b);
}
}
hts_close(out);
}
bcf_destroy1(b);
if (n_samples > 0) {
for (i = 0; i < n_samples; ++i) free(samples[i]);
free(samples);
bcf_hdr_destroy(hsub);
free(imap);
}
bcf_hdr_destroy(h);
hts_close(in);
return 0;
}
int bcf_sr_next_line(readers_t *files)
{
int32_t min_pos = INT_MAX;
int ret,i,j;
kstring_t *str = &files->tmps;
while ( min_pos==INT_MAX )
{
// Need to open new chromosome?
int eos = 0;
for (i=0; i<files->nreaders; i++)
if ( !files->readers[i].itr && !files->readers[i].nbuffer ) eos++;
if ( eos==files->nreaders )
{
const char *seq;
if ( files->targets )
{
seq = tgt_next_seq(files->targets);
if ( !seq ) return 0; // all chroms scanned
}
else
{
if ( ++files->iseq >= files->nseqs ) return 0; // all chroms scanned
seq = files->seqs[files->iseq];
}
for (i=0; i<files->nreaders; i++)
{
reader_t *reader = &files->readers[i];
if ( reader->tbx )
reader->itr = tbx_itr_querys(reader->tbx,seq);
else
reader->itr = bcf_itr_querys(reader->bcf,reader->header,seq);
}
}
// Find the smallest coordinate
for (i=0; i<files->nreaders; i++)
{
reader_t *reader = &files->readers[i];
int buffer_full = ( reader->nbuffer && reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) ? 1 : 0;
if ( reader->itr && !buffer_full )
{
// Fill the buffer with records starting at the same position
while (1)
{
if ( reader->nbuffer+1 >= reader->mbuffer )
{
reader->mbuffer += 8;
reader->buffer = (bcf1_t**) realloc(reader->buffer, sizeof(bcf1_t*)*reader->mbuffer);
for (j=8; j>0; j--)
reader->buffer[reader->mbuffer-j] = bcf_init1();
}
if ( reader->tbx )
{
ret = tbx_itr_next((BGZF*)reader->file->fp, reader->tbx, reader->itr, str);
if ( ret<0 ) break;
vcf_parse1(str, reader->header, reader->buffer[reader->nbuffer+1]);
}
else
{
ret = bcf_itr_next((BGZF*)reader->file->fp, reader->itr, reader->buffer[reader->nbuffer+1]);
if ( ret<0 ) break;
}
bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR|BCF_UN_FLT);
// apply filter
if ( reader->filter_id!=-1 && reader->buffer[reader->nbuffer+1]->d.n_flt && reader->filter_id!=reader->buffer[reader->nbuffer+1]->d.flt[0] ) continue;
set_variant_types(reader->buffer[reader->nbuffer+1]);
reader->nbuffer++;
if ( reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) break;
}
if ( ret<0 ) { tbx_itr_destroy(reader->itr); reader->itr = NULL; } // done for this chromosome
}
if ( reader->nbuffer )
{
if ( min_pos > reader->buffer[1]->pos ) min_pos = reader->buffer[1]->pos;
}
// The buffer is full - either there is nothing else to read or the last record has a different coordinate
if ( files->collapse && reader->nbuffer>2 && reader->buffer[1]->pos==reader->buffer[2]->pos )
{
collapse_buffer(files, reader);
}
}
if ( files->targets && min_pos!=INT_MAX )
{
int ret = tgt_has_position(files->targets, min_pos);
if ( ret==1 ) continue;
// The position must be skipped
if ( ret==-1 )
{
// done for this chromosome, don't read the rest
for (i=0; i<files->nreaders; i++)
{
files->readers[i].nbuffer = 0;
if ( files->readers[i].itr )
{
tbx_itr_destroy(files->readers[i].itr);
files->readers[i].itr = NULL;
}
}
min_pos = INT_MAX;
continue;
}
// remove the active line, save the buffer line
for (i=0; i<files->nreaders; i++)
{
reader_t *reader = &files->readers[i];
for (j=1; j<=reader->nbuffer; j++)
if ( reader->buffer[j]->pos!=min_pos ) break;
if ( j==1 ) continue;
if ( j<=reader->nbuffer )
{
bcf1_t *tmp = reader->buffer[1]; reader->buffer[1] = reader->buffer[j]; reader->buffer[j] = tmp;
reader->nbuffer = 1;
}
else
reader->nbuffer = 0;
}
min_pos = INT_MAX;
}
}
//printf("[next_line] min_pos=%d\n", min_pos+1);
//debug_buffers(files);
// Set the current line
ret = 0;
bcf1_t *first = NULL;
for (i=0; i<files->nreaders; i++)
{
reader_t *reader = &files->readers[i];
if ( !reader->nbuffer || reader->buffer[1]->pos!=min_pos ) continue;
// Match the records by REF and ALT
int j, irec = -1;
if ( first )
{
for (j=1; j<=reader->nbuffer; j++)
{
bcf1_t *line = reader->buffer[j];
if ( min_pos != line->pos ) break; // done with this buffer
if ( files->collapse&COLLAPSE_ANY ) { irec=j; break; } // checking position only
if ( files->collapse&COLLAPSE_SNPS && first->d.var_type&VCF_SNP && line->d.var_type&VCF_SNP ) { irec=j; break; }
if ( files->collapse&COLLAPSE_INDELS && first->d.var_type&VCF_INDEL && line->d.var_type&VCF_INDEL ) { irec=j; break; }
if ( first->rlen != line->rlen ) continue; // REFs do not match
if ( strcmp(first->d.allele[0], line->d.allele[0]) ) continue; // REFs do not match
int ial,jal;
if ( files->collapse==COLLAPSE_NONE )
{
// require exact match, all alleles must be identical
if ( first->n_allele!=line->n_allele ) continue; // different number of alleles
int nmatch = 1; // REF has been already checked
for (ial=1; ial<first->n_allele; ial++)
{
for (jal=1; jal<line->n_allele; jal++)
if ( !strcmp(first->d.allele[ial], line->d.allele[jal]) ) { nmatch++; break; }
}
if ( nmatch>=first->n_allele ) { irec=j; break; }
}
else
{
// thorough check: the REFs and some of the alleles have to be shared
// (neglecting different representations of the same indel for now)
for (ial=1; ial<first->n_allele; ial++)
{
for (jal=1; jal<line->n_allele; jal++)
if ( !strcmp(first->d.allele[ial], line->d.allele[jal]) ) { irec=j; break; }
if ( irec>=1 ) break;
}
}
if ( irec>=1 ) break;
}
if ( irec==-1 ) continue;
}
else
{
first = reader->buffer[1];
irec = 1;
}
bcf1_t *tmp = reader->buffer[0];
reader->buffer[0] = reader->buffer[irec];
for (j=irec+1; j<=reader->nbuffer; j++)
reader->buffer[j-1] = reader->buffer[j];
reader->buffer[ reader->nbuffer ] = tmp;
reader->nbuffer--;
ret |= 1<<i;
}
// fprintf(stdout,"[next_line] min_pos=%d mask=%d\n", min_pos+1, ret);
// debug_buffers(stdout,files);
return ret;
}
static int query_regions(args_t *args, char *fname, char **regs, int nregs)
{
int i;
htsFile *fp = hts_open(fname,"r");
if ( !fp ) error("Could not read %s\n", fname);
enum htsExactFormat format = hts_get_format(fp)->format;
regidx_t *reg_idx = NULL;
if ( args->targets_fname )
{
reg_idx = regidx_init(args->targets_fname, NULL, NULL, 0, NULL);
if ( !reg_idx ) error("Could not read %s\n", args->targets_fname);
}
if ( format == bcf )
{
htsFile *out = hts_open("-","w");
if ( !out ) error("Could not open stdout\n", fname);
hts_idx_t *idx = bcf_index_load(fname);
if ( !idx ) error("Could not load .csi index of %s\n", fname);
bcf_hdr_t *hdr = bcf_hdr_read(fp);
if ( !hdr ) error("Could not read the header: %s\n", fname);
if ( args->print_header )
bcf_hdr_write(out,hdr);
if ( !args->header_only )
{
bcf1_t *rec = bcf_init();
for (i=0; i<nregs; i++)
{
hts_itr_t *itr = bcf_itr_querys(idx,hdr,regs[i]);
while ( bcf_itr_next(fp, itr, rec) >=0 )
{
if ( reg_idx && !regidx_overlap(reg_idx, bcf_seqname(hdr,rec),rec->pos,rec->pos+rec->rlen-1, NULL) ) continue;
bcf_write(out,hdr,rec);
}
tbx_itr_destroy(itr);
}
bcf_destroy(rec);
}
if ( hts_close(out) ) error("hts_close returned non-zero status for stdout\n");
bcf_hdr_destroy(hdr);
hts_idx_destroy(idx);
}
else if ( format==vcf || format==sam || format==unknown_format )
{
tbx_t *tbx = tbx_index_load(fname);
if ( !tbx ) error("Could not load .tbi/.csi index of %s\n", fname);
kstring_t str = {0,0,0};
if ( args->print_header )
{
while ( hts_getline(fp, KS_SEP_LINE, &str) >= 0 )
{
if ( !str.l || str.s[0]!=tbx->conf.meta_char ) break;
puts(str.s);
}
}
if ( !args->header_only )
{
int nseq;
const char **seq = NULL;
if ( reg_idx ) seq = tbx_seqnames(tbx, &nseq);
for (i=0; i<nregs; i++)
{
hts_itr_t *itr = tbx_itr_querys(tbx, regs[i]);
if ( !itr ) continue;
while (tbx_itr_next(fp, tbx, itr, &str) >= 0)
{
if ( reg_idx && !regidx_overlap(reg_idx,seq[itr->curr_tid],itr->curr_beg,itr->curr_end, NULL) ) continue;
puts(str.s);
}
tbx_itr_destroy(itr);
}
free(seq);
}
free(str.s);
tbx_destroy(tbx);
}
else if ( format==bam )
error("Please use \"samtools view\" for querying BAM files.\n");
if ( reg_idx ) regidx_destroy(reg_idx);
if ( hts_close(fp) ) error("hts_close returned non-zero status: %s\n", fname);
for (i=0; i<nregs; i++) free(regs[i]);
free(regs);
return 0;
}
