/**
* 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;
};
/**
* Reads next record, hides the random access of different regions from the user.
*/
bool BAMOrderedReader::read(bam1_t *s)
{
if (random_access_enabled)
{
while(true)
{
if (itr && bam_itr_next(sam, itr, s)>=0)
{
return true;
}
else if (!initialize_next_interval())
{
return false;
}
}
}
else
{
if (bam_read1(sam->fp.bgzf, s)>=0)
{
//todo: filter via interval tree
//if found in tree, return true else false
return true;
}
else
{
return false;
}
}
return false;
};
/**
* Reads next record, hides the random access of different regions from the user.
*/
bool TBXOrderedReader::read(kstring_t *s)
{
if (random_access_enabled)
{
while(true)
{
if (itr && tbx_itr_next(hts, tbx, itr, s)>=0)
{
return true;
}
else if (!initialize_next_interval())
{
return false;
}
}
}
else
{
if (hts_getline(hts, '\n', s) >= 0)
{
return true;
}
else
{
return false;
}
}
return false;
};
/**
* Ensures that buffer for each file contains at least records of 2 different positions
* Updates the latest position. [store latest and second latest]
* returns false when all files are read through.
* Note that these bcf1_t memory allocation are handled by BCFSyncedStreamReader.
*/
bool BCFSyncedStreamReader::read_next_position(std::vector<bcfptr*>& current_recs)
{
//put records in pool
for (uint32_t i=0; i<current_recs.size(); ++i)
{
store_bcf1_into_pool(current_recs[i]->v);
delete(current_recs[i]);
}
current_recs.clear();
//process records in priority queue or initialize next interval if pq is empty
//initialize_next_interval tops up the pq
if (pq.size()!=0 || initialize_next_interval())
{
//dequeue pqueue most recent position and return it
bcfptr* variant = pq.top();
bcfptr* cvariant = variant;
while (bcfptr_scmp(cvariant, variant)==0)
{
bcfptr *b = pq.top();
current_recs.push_back(b);
buffer[b->file_index].remove(b->v);
fill_buffer(b->file_index);
pq.pop();
if (pq.size()==0)
{
break;
}
else
{
cvariant = pq.top();
}
}
//current_pos1 = current_recs.front().pos1;
return true;
}
else //end of contig or eof for all files
{
return false;
}
}
