/usr/include/ncbi-vdb/sra/abi.h

/*===========================================================================
*
*                            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_abi_
#define _h_sra_abi_

#ifndef _h_sra_rd_extern_
#include <sra/rd-extern.h>
#endif

#ifndef _h_sra_sradb_
#include <sra/sradb.h>
#endif

#ifdef __cplusplus
extern "C" {
#endif

/*--------------------------------------------------------------------------
 * AbsolidReader
 */
typedef struct AbsolidReader AbsolidReader;

/* Make
 *  create AbsolidReader reference based
 *  on opened table and properties:
 *     table      - SRATable
 *     accession  - accession
 *     minReadLen - minimal length of the outputed read, 0 - no minimum (FUSE)
 *     origFormat - excludes SRR accession & length on defline
 *     noclip     - don't clip quality left and right
 *     minSpotId  - starting spot id, 0 - ignored (run information used)
 *     maxSpotId  - ending spot id, 0 - ignored (run information used)
 *                  you cannot seek out of range of [minSpotId:maxSpotId]
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderMake(const AbsolidReader** self, const SRATable* table,
                                        const char* accession, bool origFormat,
                                        bool noClip, uint32_t minReadLen,
                                        spotid_t minSpotId, spotid_t maxSpotId, bool signal);

/* Whack
 *  releases object obtained from AbsolidReaderMake
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderWhack(const AbsolidReader* self);

/* FirstSpot
 *  set current spot to first in the run
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderFirstSpot(const AbsolidReader* self);

/* SeekSpot
 *  set current spot
 * if error occurred current spot position becomes 0
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderSeekSpot(const AbsolidReader* self, spotid_t spot);

/* NextSpot
 *  Seek to next spot from current
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderNextSpot(const AbsolidReader* self);

/* CurrentSpot
 *  Get current spot
 *  sopt [OUT] - pointer to assign value of the current spot
 * returns GetRCState(rc) == rcExhausted when out of spots
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderCurrentSpot(const AbsolidReader* 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)
 */
SRA_RD_EXTERN rc_t CC AbsolidReader_SpotInfo(const AbsolidReader* 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)
 *  cskey     [OUT] - pointer to assign value of the read color space key (can be NULL)
 *  if start and len is == 0 read is empty
 */
SRA_RD_EXTERN rc_t CC AbsolidReader_SpotReadInfo(const AbsolidReader* 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);

/* SpotPrefix
 *  retrieve current spot name prefix
 *  prefix [OUT] - pointer to assign value of the spot name prefix
 *  prefix_sz [OUT] - pointer to assign value of the length of the spot name prefix
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderSpotName(const AbsolidReader* self,
                                            const char** prefix, size_t* prefix_sz,
                                            const char** suffix, size_t* suffix_sz);

/* BaseName
 *  retrieve name string for the spot, result always has '\0' at the and (asciiz string)
 *  readid [IN] - 1-based, if <= 0 than the whole spot, otherwise particular read
 *  label  [IN] - overrides read label appending (printLabel), set to NULL by default
 *  data   [IN] - pointer to buffer for printing
 *  dsize  [IN] - data buffer size
 *  written [IN,OUT] - optional number of bytes occupied by string
 *                     (not including the trailing '\0' used to end output), may by more than dsize
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderHeader(const AbsolidReader* self, uint32_t readId,
                                          char* data, size_t dsize, size_t* written);

/* Base
 *  retrieve bases for the spot
 *  other parameters see description for AbsolidReaderBaseName above
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderBase(const AbsolidReader* self, uint32_t readId,
                                        char* data, size_t dsize, size_t* written);

/* Quality
 *  retrieve quality string for the spot
 *  other parameters see description for AbsolidReaderBaseName above
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderQuality(const AbsolidReader* self, uint32_t readId,
                                           char* data, size_t dsize, size_t* written);

/* Signals
 *  retrieve signal string for the spot
 *  other parameters see description for AbsolidReaderBaseName above
 */
SRA_RD_EXTERN rc_t CC AbsolidReaderSignalFTC(const AbsolidReader* self, uint32_t readId,
                                             char* data, size_t dsize, size_t* written);
SRA_RD_EXTERN rc_t CC AbsolidReaderSignalCY3(const AbsolidReader* self, uint32_t readId,
                                             char* data, size_t dsize, size_t* written);
SRA_RD_EXTERN rc_t CC AbsolidReaderSignalTXR(const AbsolidReader* self, uint32_t readId,
                                             char* data, size_t dsize, size_t* written);
SRA_RD_EXTERN rc_t CC AbsolidReaderSignalCY5(const AbsolidReader* self, uint32_t readId,
                                             char* data, size_t dsize, size_t* written);
#ifdef __cplusplus
}
#endif

#endif /* _h_sra_abi_ */
libncbi-vdb-dev 2.8.1+dfsg-2 / usr / include / ncbi-vdb / sra / abi.h
