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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef _h_sra_reader_
#define _h_sra_reader_
#ifndef _h_sra_sradb_
#include <sra/sradb.h>
#endif
#define SRAREADER_COL_MANDATORY 0x00
#define SRAREADER_COL_OPTIONAL 0x01
typedef struct SRAReaderColumn_struct {
uint32_t opt;
const char* name;
const char* datatype;
const SRAColumn* col;
const void* base;
bitsz_t size;
} SRAReaderColumn;
typedef struct SRAReader_struct {
char* accession;
const SRATable* table;
spotid_t minSpotId;
spotid_t maxSpotId;
uint32_t options;
SRAReaderColumn cols[64]; /* max of 64 columns, must be enough, last one must have NULL name */
/* current spot data */
spotid_t spot;
const SRAReaderColumn* spot_name;
const INSDC_coord_len** spot_len;
const INSDC_coord_zero** read_start;
const INSDC_coord_len** read_len;
const bitsz_t* read_len_size;
const SRAReadTypes** read_type;
const char** label;
const INSDC_coord_zero** label_start;
const INSDC_coord_len** label_len;
} SRAReader;
/* Common macro for self pointer and current spot state validation */
#define CHECK_SELF(ObjType) \
ObjType* me = (ObjType*)self; \
if(self == NULL) { \
return RC(rcSRA, rcFormatter, rcAccessing, rcSelf, rcNull); \
}
#define CHECK_SPOT(Obj) \
if( (Obj).spot < (Obj).minSpotId ) { \
return RC(rcSRA, rcFormatter, rcAccessing, rcRow, rcUnknown); \
} \
if( (Obj).spot > (Obj).maxSpotId ) { \
return RC(rcSRA, rcFormatter, rcAccessing, rcRow, rcExhausted); \
}
rc_t SRAReaderMake(const SRAReader** self, size_t size, const SRATable* table,
const char* accession, spotid_t minSpotId, spotid_t maxSpotId);
rc_t SRAReaderInit(const SRAReader* self, int options, const SRAReaderColumn* const cols);
/* Whack
* releases object obtained from SRAReaderMake
* or AddRef ( see above )
*/
rc_t SRAReaderWhack(const SRAReader *self);
/* FindColData
* find OPENED column by it's definition and return it's base pointer or col struct
*/
rc_t SRAReader_FindColData(const SRAReader* self, const SRAReaderColumn* definition, const SRAReaderColumn** col, const void*** base);
/* FirstSpot
* set current spot to first in the run
*/
rc_t SRAReaderFirstSpot(const SRAReader* self);
/* SeekSpot
* set current spot
* if error occurred current spot position becomes 0
*/
rc_t SRAReaderSeekSpot(const SRAReader* self, spotid_t spot);
/* NextSpot
* Seek to next spot from current
*/
rc_t SRAReaderNextSpot(const SRAReader* self);
/* CurrentSpot
* Get current spot
* sopt [OUT] - pointer to assign value of the current spot
* returns GetRCState(rc) == rcExhausted when out of spots
*/
rc_t SRAReaderCurrentSpot(const SRAReader* self, spotid_t* spot);
/* SpotInfo
* Get current spot information
* spotname [OUT] - pointer to assign value of the current spot name (can be NULL)
* spotname_sz [OUT] - pointer to assign value of the length of the spot name (can be NULL)
* spot_len [OUT] - pointer to assign value of the current spot length (can be NULL)
* num_reads[OUT] - pointer to assign value of the number of reads in current spot (can be NULL)
*/
rc_t SRAReader_SpotInfo(const SRAReader* self, const char** spotname, size_t* spotname_sz,
uint32_t* spot_len, uint32_t* num_reads);
/* SpotReadInfo
* Get read information for current spot
* readid [IN] - 1-based read id
* read_type [OUT] - pointer to assign value of the read type (can be NULL)
* read_label[OUT] - pointer to assign value of the read label (can be NULL)
* read_label_sz [OUT] - pointer to assign value of the length of the read label (can be NULL)
* read_start[OUT] - pointer to assign value of the read start in spot (can be NULL)
* read_len [OUT] - pointer to assign value of the read length (can be NULL)
* if start and len is == 0 read is empty
*/
rc_t SRAReader_SpotReadInfo(const SRAReader* self, uint32_t readId, SRAReadTypes* read_type,
const char** read_label, INSDC_coord_len* read_label_sz,
INSDC_coord_zero* read_start, INSDC_coord_len* read_len);
/* GetCurrentSpotData
* retrieve current spot data as a blob
* data [IN] - pointer to buffer for printing
* dsize [IN] - data buffer size
* written [IN,OUT] - optional number of bytes occupied by buffer, may by more than dsize
* MUST BE SEPARATELY DEFINED for each reader format
*/
rc_t SRAReader_GetCurrentSpotData(const SRAReader* self, char *data, size_t dsize, size_t* written);
/* GetNextSpotData (streaming function)
* move to the next spot and retrieve current spot data as a blob
* data [IN] - pointer to buffer for printing
* dsize [IN] - data buffer size
* written [IN,OUT] - optional number of bytes occupied by buffer, may by more than dsize
* MUST BE SEPARATELY DEFINED for each reader format
*/
rc_t SRAReader_GetNextSpotData(const SRAReader* self, char *data, size_t dsize, size_t* written);
#endif /* _h_sra_reader_ */
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