Exemplos de get_bcf1_from_pool em C++ (Cpp)

Exemplo n.º 1

Arquivo: bcf_synced_sreader.cpp Projeto: amarawi/gotcloud

/**
 * Gets records for the most recent position and fills up the buffer from file i.
 * returns true if buffer is filled or it is not necessary to fill buffer.
 * returns false if no more records are found to fill buffer
 */
void BCFSyncedStreamReader::fill_buffer(int32_t i)
{
    //not necessary to fill buffer
    if (buffer[i].size()>=2)
        return;

    int32_t pos1 = buffer[i].size()==0 ? 0 : bcf_get_pos1(buffer[i].front());

    if (ftypes[i]==FT_BCF_GZ)
    {
        bcf1_t *v = get_bcf1_from_pool();
        bool populated = false;
        while (itrs[i] && bcf_itr_next(vcfs[i], itrs[i], v) >= 0)
        {
            populated = true;
            bcf_unpack(v, BCF_UN_STR);
            buffer[i].push_back(v);
            insert_into_pq(i, v);

            if (pos1==0)
            {
                pos1 = bcf_get_pos1(v);
            }

            if (bcf_get_pos1(v)!=pos1)
            {
                break;
            }
            v = get_bcf1_from_pool();
            populated = false;
        }
        if (!populated)
            store_bcf1_into_pool(v);
    }
    else if (ftypes[i]==FT_VCF_GZ)
    {
        while (itrs[i] && tbx_itr_next(vcfs[i], tbxs[i], itrs[i], &s) >= 0)
        {
            bcf1_t *v = get_bcf1_from_pool();
            vcf_parse(&s, hdrs[i], v);

            bcf_unpack(v, BCF_UN_STR);
            buffer[i].push_back(v);
            insert_into_pq(i, v);

            if (pos1==0)
            {
                pos1 = bcf_get_pos1(v);
            }

            if (bcf_get_pos1(v)!=pos1)
            {
                break;
            }
        }
    }
}

Exemplo n.º 2

Arquivo: bcf_synced_reader.cpp Projeto: holtgrewe/vt

/**
 * Gets records for the most recent position and fills up the buffer from file i.
 * returns true if buffer is filled or it is not necessary to fill buffer.
 * returns false if no more records are found to fill buffer
 */
void BCFSyncedReader::fill_buffer(int32_t i)
{
    if (buffer[i].size()>=2)
        return;

    if (random_access)
    {
        int32_t pos1 = buffer[i].size()==0 ? 0 : bcf_get_pos1(buffer[i].front());

        if (ftypes[i].format==bcf)
        {
            bcf1_t *v = get_bcf1_from_pool();
            bool populated = false;

            while (itrs[i] && bcf_itr_next(files[i], itrs[i], v)>=0)
            {
                populated = true;
                bcf_unpack(v, BCF_UN_STR);
                
                //check to ensure order
                if (!buffer[i].empty())
                {
                    if (!bcf_is_in_order(buffer[i].back(), v))
                    {
                        fprintf(stderr, "[E:%s:%d %s] VCF file not in order: %s\n", __FILE__, __LINE__, __FUNCTION__, file_names[i].c_str());
                        exit(1);
                    }
                }
                
                buffer[i].push_back(v);
                insert_into_pq(i, v);

                if (pos1==0)
                {
                    pos1 = bcf_get_pos1(v);
                }

                if (bcf_get_pos1(v)!=pos1)
                {
                    break;
                }

                v = get_bcf1_from_pool();
                populated = false;
            }

            if (!populated)
                store_bcf1_into_pool(v);
        }
        else if (ftypes[i].format==vcf)
        {
            while (itrs[i] && tbx_itr_next(files[i], tbxs[i], itrs[i], &s)>=0)
            {
                bcf1_t *v = get_bcf1_from_pool();
                vcf_parse(&s, hdrs[i], v);

                bcf_unpack(v, BCF_UN_STR);
                
                //check to ensure order
                if (!buffer[i].empty())
                {
                    if (!bcf_is_in_order(buffer[i].back(), v))
                    {
                        fprintf(stderr, "[E:%s:%d %s] VCF file not in order: %s\n", __FILE__, __LINE__, __FUNCTION__, file_names[i].c_str());
                        exit(1);
                    }
                }
                
                buffer[i].push_back(v);
                insert_into_pq(i, v);

                if (pos1==0)
                {
                    pos1 = bcf_get_pos1(v);
                }

                if (bcf_get_pos1(v)!=pos1)
                {
                    break;
                }
            }
        }
    }
    else
    {
        int32_t rid = buffer[i].size()==0 ? -1 : bcf_get_rid(buffer[i].front());
        int32_t pos1 = buffer[i].size()==0 ? 0 : bcf_get_pos1(buffer[i].front());

        bcf1_t *v = get_bcf1_from_pool();
        bool populated = false;

        while (bcf_read(files[i], hdrs[i], v)>=0)
        {
            populated = true;
            bcf_unpack(v, BCF_UN_STR);
            
            //check to ensure order
            if (!buffer[i].empty())
            {
                if (!bcf_is_in_order(buffer[i].back(), v))
                {
                    fprintf(stderr, "[E:%s:%d %s] VCF file not in order: %s\n", __FILE__, __LINE__, __FUNCTION__, file_names[i].c_str());
                    exit(1);
                }
            }
            
            buffer[i].push_back(v);
            insert_into_pq(i, v);

            if (rid==-1)
            {
                rid = bcf_get_rid(v);
                pos1 = bcf_get_pos1(v);
            }

            if (bcf_get_rid(v)!=rid || bcf_get_pos1(v)!=pos1)
            {
                break;
            }

            v = get_bcf1_from_pool();
            populated = false;
        }

        if (!populated)
            store_bcf1_into_pool(v);
    }
}