static size_t CC ext_rec_size ( struct VCursor const *curs, int64_t row_id, void *data )
{
size_t res = 0;
uint32_t q_len;
rc_t rc = read_base_and_len( curs, "QUALITY", row_id, NULL, &q_len );
if ( rc == 0 )
{
ext_rec * rec;
res = ( sizeof *rec ) + q_len;
}
return res;
}
static rc_t CC ext_rec_populate ( void *obj,
const PlacementRecord *placement, struct VCursor const *curs,
INSDC_coord_zero ref_window_start, INSDC_coord_len ref_window_len,
void *data )
{
const bool * orientation;
rc_t rc = read_base_and_len( curs, "REF_ORIENTATION", placement->id, (const void **)&orientation, NULL );
if ( rc == 0 )
{
uint8_t * quality;
uint32_t quality_len;
ext_rec * rec = ( ext_rec * ) obj;
rec->reverse = *orientation;
rc = read_base_and_len( curs, "QUALITY", placement->id, (const void **)&quality, &quality_len );
if ( rc == 0 )
{
rec->quality = ( uint8_t * )rec;
rec->quality += sizeof ( * rec );
memcpy( rec->quality, quality, quality_len );
}
}
return rc;
}
static rc_t CC alloc_size( struct VCursor const *curs, int64_t row_id, size_t * size,
void *data, void * placement_ctx )
{
rc_t rc = 0;
walker_rec * rec;
struct ref_walker * walker = data;
walker_col_ids * col_ids = placement_ctx;
*size = ( sizeof *rec );
if ( !walker->omit_quality )
{
uint32_t q_len;
rc = read_base_and_len( curs, col_ids->idx_quality, row_id, NULL, &q_len );
if ( rc == 0 )
*size += q_len;
}
return rc;
}
static rc_t CC populate_data( void *obj, const PlacementRecord *placement,
struct VCursor const *curs, INSDC_coord_zero ref_window_start, INSDC_coord_len ref_window_len,
void *data, void * placement_ctx )
{
walker_rec * rec = obj;
struct ref_walker * walker = data;
walker_col_ids * col_ids = placement_ctx;
rc_t rc = 0;
rec->quality = NULL;
if ( !walker->process_dups )
{
const uint8_t * read_filter;
uint32_t read_filter_len;
rc = read_base_and_len( curs, col_ids->idx_read_filter, placement->id,
(const void **)&read_filter, &read_filter_len );
if ( rc == 0 )
{
if ( ( *read_filter == SRA_READ_FILTER_REJECT )||
( *read_filter == SRA_READ_FILTER_CRITERIA ) )
{
rc = RC( rcAlign, rcType, rcAccessing, rcId, rcIgnored );
}
}
}
if ( rc == 0 )
{
const bool * orientation;
rc = read_base_and_len( curs, col_ids->idx_ref_orientation, placement->id,
(const void **)&orientation, NULL );
if ( rc == 0 )
rec->reverse = *orientation;
}
if ( rc == 0 && !walker->omit_quality )
{
const uint8_t * quality;
uint32_t quality_len;
rc = read_base_and_len( curs, col_ids->idx_quality, placement->id,
(const void **)&quality, &quality_len );
if ( rc == 0 )
{
rec->quality = ( uint8_t * )rec;
rec->quality += sizeof ( * rec );
memcpy( rec->quality, quality, quality_len );
}
}
if ( rc == 0 && walker->read_tlen )
{
const int32_t * tlen;
uint32_t tlen_len;
rc = read_base_and_len( curs, col_ids->idx_template_len, placement->id,
(const void **)&tlen, &tlen_len );
if ( rc == 0 && tlen_len > 0 )
rec->tlen = *tlen;
else
rec->tlen = 0;
}
else
rec->tlen = 0;
return rc;
}
