/**
* Reads next record, hides the random access of different regions from the user.
*/
bool BCFOrderedReader::read(bcf1_t *v)
{
if (random_access_enabled)
{
if (ftype.format==bcf)
{
while(true)
{
if (itr && bcf_itr_next(file, itr, v)>=0)
{
return true;
}
else if (!initialize_next_interval())
{
return false;
}
}
}
else
{
while(true)
{
if (itr && tbx_itr_next(file, tbx, itr, &s)>=0)
{
vcf_parse1(&s, hdr, v);
return true;
}
else if (!initialize_next_interval())
{
return false;
}
}
}
}
else
{
if (bcf_read(file, hdr, v)==0)
{
return true;
}
else
{
return false;
}
}
return false;
};
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;
}
/*
* _reader_fill_buffer() - buffers all records with the same coordinate
*/
static void _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader)
{
// Return if the buffer is full: the coordinate of the last buffered record differs
if ( reader->nbuffer && reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) return;
// No iterator (sequence not present in this file) and not streaming
if ( !reader->itr && !files->streaming ) return;
// Fill the buffer with records starting at the same position
int i, ret = 0;
while (1)
{
if ( reader->nbuffer+1 >= reader->mbuffer )
{
// Increase buffer size
reader->mbuffer += 8;
reader->buffer = (bcf1_t**) realloc(reader->buffer, sizeof(bcf1_t*)*reader->mbuffer);
for (i=8; i>0; i--) // initialize
{
reader->buffer[reader->mbuffer-i] = bcf_init1();
reader->buffer[reader->mbuffer-i]->max_unpack = files->max_unpack;
reader->buffer[reader->mbuffer-i]->pos = -1; // for rare cases when VCF starts from 1
}
}
if ( files->streaming )
{
if ( reader->file->format.format==vcf )
{
if ( (ret=hts_getline(reader->file, KS_SEP_LINE, &files->tmps)) < 0 ) break; // no more lines
int ret = vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]);
if ( ret<0 ) break;
}
else if ( reader->file->format.format==bcf )
{
if ( (ret=bcf_read1(reader->file, reader->header, reader->buffer[reader->nbuffer+1])) < 0 ) break; // no more lines
}
else
{
fprintf(stderr,"[%s:%d %s] fixme: not ready for this\n", __FILE__,__LINE__,__FUNCTION__);
exit(1);
}
}
else if ( reader->tbx_idx )
{
if ( (ret=tbx_itr_next(reader->file, reader->tbx_idx, reader->itr, &files->tmps)) < 0 ) break; // no more lines
vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]);
}
else
{
if ( (ret=bcf_itr_next(reader->file, reader->itr, reader->buffer[reader->nbuffer+1])) < 0 ) break; // no more lines
bcf_subset_format(reader->header,reader->buffer[reader->nbuffer+1]);
}
// apply filter
if ( !reader->nfilter_ids )
bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR);
else
{
bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR|BCF_UN_FLT);
if ( !has_filter(reader, reader->buffer[reader->nbuffer+1]) ) continue;
}
reader->nbuffer++;
if ( reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) break; // the buffer is full
}
if ( ret<0 )
{
// done for this region
tbx_itr_destroy(reader->itr);
reader->itr = NULL;
}
if ( files->collapse && reader->nbuffer>=2 && reader->buffer[1]->pos==reader->buffer[2]->pos )
collapse_buffer(files, reader);
}