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Make repeated seeks possible #1363

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Jan 4, 2022
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Make repeated seeks possible #1363

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24 changes: 21 additions & 3 deletions synced_bcf_reader.c
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,7 @@ static int _regions_add(bcf_sr_regions_t *reg, const char *chr, hts_pos_t start,
static bcf_sr_regions_t *_regions_init_string(const char *str);
static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *rec);
static void _regions_sort_and_merge(bcf_sr_regions_t *reg);
static int _bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, hts_pos_t start, hts_pos_t end, int missed_reg_handler);

char *bcf_sr_strerror(int errnum)
{
Expand Down Expand Up @@ -838,6 +839,7 @@ static void bcf_sr_seek_start(bcf_srs_t *readers)
for (i=0; i<reg->nseqs; i++)
reg->regs[i].creg = -1;
reg->iseq = 0;
reg->prev_seq = -1;
}


Expand All @@ -851,8 +853,18 @@ int bcf_sr_seek(bcf_srs_t *readers, const char *seq, hts_pos_t pos)
bcf_sr_seek_start(readers);
return 0;
}
bcf_sr_regions_overlap(readers->regions, seq, pos, pos);

int i, nret = 0;

// Need to position both the readers and the regions. The latter is a bit of a mess
// because we can have in memory or external regions. The safe way is:
// - reset all regions as if they were not read from at all (bcf_sr_seek_start)
// - find the requested iseq (stored in the seq_hash)
// - position regions to the requested position (bcf_sr_regions_overlap)
bcf_sr_seek_start(readers);
if ( khash_str2int_get(readers->regions->seq_hash, seq, &i)>=0 ) readers->regions->iseq = i;
_bcf_sr_regions_overlap(readers->regions, seq, pos, pos, 0);

for (i=0; i<readers->nreaders; i++)
{
nret += _reader_seek(&readers->readers[i],seq,pos,MAX_CSI_COOR-1);
Expand Down Expand Up @@ -1406,14 +1418,20 @@ static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *re
}

int bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, hts_pos_t start, hts_pos_t end)
{
return _bcf_sr_regions_overlap(reg,seq,start,end,1);
}

static int _bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, hts_pos_t start, hts_pos_t end, int missed_reg_handler)
{
int iseq;
if ( khash_str2int_get(reg->seq_hash, seq, &iseq)<0 ) return -1; // no such sequence
if ( missed_reg_handler && !reg->missed_reg_handler ) missed_reg_handler = 0;

if ( reg->prev_seq==-1 || iseq!=reg->prev_seq || reg->prev_start > start ) // new chromosome or after a seek
{
// flush regions left on previous chromosome
if ( reg->missed_reg_handler && reg->prev_seq!=-1 && reg->iseq!=-1 )
if ( missed_reg_handler && reg->prev_seq!=-1 && reg->iseq!=-1 )
bcf_sr_regions_flush(reg);

bcf_sr_regions_seek(reg, seq);
Expand All @@ -1427,7 +1445,7 @@ int bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, hts_pos_t sta
{
if ( bcf_sr_regions_next(reg) < 0 ) return -2; // no more regions left
if ( reg->iseq != iseq ) return -1; // does not overlap any regions
if ( reg->missed_reg_handler && reg->end < start ) reg->missed_reg_handler(reg, reg->missed_reg_data);
if ( missed_reg_handler && reg->end < start ) reg->missed_reg_handler(reg, reg->missed_reg_data);
}
if ( reg->start <= end ) return 0; // region overlap
return -1; // no overlap
Expand Down