static rc_t write_to_sorter( struct sorter * sorter, int64_t seq_spot_id, uint32_t seq_read_id,
const String * unpacked_bases )
{
/* we write it to the store...*/
rc_t rc;
const String * to_store;
pack_4na( unpacked_bases, &sorter->buf );
rc = StringCopy( &to_store, &sorter->buf.S );
if ( rc != 0 )
ErrMsg( "StringCopy() -> %R", rc );
else
{
uint64_t key = make_key( seq_spot_id, seq_read_id );
rc = KVectorSetPtr( sorter->store, key, (const void *)to_store );
if ( rc != 0 )
ErrMsg( "KVectorSetPtr() -> %R", rc );
else
{
size_t item_size = ( sizeof key ) + ( sizeof *to_store ) + to_store->size;
sorter->bytes_in_store += item_size;
}
}
if ( rc == 0 &&
sorter->params.mem_limit > 0 &&
sorter->bytes_in_store >= sorter->params.mem_limit )
rc = save_store( sorter );
return rc;
}
static bool rr_store_alignment( rr_store * rr, int64_t align_id, const VCursor * curs, uint32_t read_idx )
{
bool res = false;
const INSDC_4na_bin * read = NULL;
uint32_t read_len;
rc_t rc = VCursorCellDataDirect( curs, align_id, read_idx, NULL, ( const void** ) &read, NULL, &read_len );
if ( rc == 0 )
{
rr_entry * entry;
res = rr_entry_make ( &entry, read, read_len );
if ( res )
{
uint64_t key = ( uint64_t ) align_id;
res = ( KVectorSetPtr ( rr -> v, key, entry ) == 0 );
if ( !res )
rr_entry_release( key, entry, NULL );
}
}
return res;
}
