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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_illumina_
#define _h_sra_illumina_
#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
/*--------------------------------------------------------------------------
* IlluminaReader
*/
typedef struct IlluminaReader IlluminaReader;
/* Make
* create IlluminaReader reference based
* on opened table and properties:
* table - SRATable
* accession - accession
* read - output reads
* qual1 - output quality1
* qual4 - output quality4
* intensity - output intensity
* noise - output noise
* signal - output signal
* qseq - output QSEQ format
* 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 IlluminaReaderMake(const IlluminaReader** self, const SRATable* table, const char* accession,
bool read, bool qual1, bool qual4,
bool intensity, bool noise, bool signal, bool qseq,
spotid_t minSpotId, spotid_t maxSpotId);
/* Whack
* releases object obtained from IlluminaReaderMake
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderWhack(const IlluminaReader* self);
/* FirstSpot
* set current spot to first in the run
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderFirstSpot(const IlluminaReader* self);
/* SeekSpot
* set current spot
* if error occurred current spot position becomes 0
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderSeekSpot(const IlluminaReader* self, spotid_t spot);
/* NextSpot
* Seek to next spot from current
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderNextSpot(const IlluminaReader* 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 IlluminaReaderCurrentSpot(const IlluminaReader* self, spotid_t *spot);
/* SpotInfo
* Get current spot information
* spotname [OUT] - pointer to assign value of the current 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 IlluminaReader_SpotInfo(const IlluminaReader* self,
const char** spotname, size_t* spotname_sz,
INSDC_coord_val* lane, INSDC_coord_val* tile,
INSDC_coord_val* x, INSDC_coord_val* y,
uint32_t* spot_len, uint32_t* num_reads);
/* SpotReadInfo
* Get read information for current spot
* readid [IN] - 1-based read id
* read_label[OUT] - pointer to assign value of the read label (can be NULL)
* read_type [OUT] - pointer to assign value of the read type (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 IlluminaReader_SpotReadInfo(const IlluminaReader* 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);
/* Base
* retrieve bases for the spot, result always has '\0' at the and (asciiz string)
* 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 IlluminaReaderBase(const IlluminaReader* self, char* data, size_t dsize, size_t* written);
/* Noise
* retrieve noise in 4 floats per base format
* other parameters see description for IlluminaReaderBase above
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderNoise(const IlluminaReader* self, char* data, size_t dsize, size_t* written);
/* Intensity
* retrieve intensity in 4 floats per base format
* other parameters see description for IlluminaReaderBase above
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderIntensity(const IlluminaReader* self, char* data, size_t dsize, size_t* written);
/* Signal
* retrieve signal in 4 floats per base format
* other parameters see description for IlluminaReaderBase above
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderSignal(const IlluminaReader* self, char* data, size_t dsize, size_t* written);
/* Quality (BINARY)
* retrieve quality as single bytes per bases
* readid [IN] - 1-based, if <= 0 than the whole spot, otherwise particular read
* other parameters see description for IlluminaReaderBase above
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderQuality1(const IlluminaReader* self, uint32_t readId, char* data, size_t dsize, size_t* written);
/* Quality
* retrieve quality in 4 integers per base format
* other parameters see description for IlluminaReaderBase above
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderQuality4(const IlluminaReader* self, char* data, size_t dsize, size_t* written);
/* QSeq
* spot information as in QSEQ format
* other parameters see description for IlluminaReaderBase above
*/
SRA_RD_EXTERN rc_t CC IlluminaReaderQSeq(const IlluminaReader* self, uint32_t readId, bool spot_group,
char* data, size_t dsize, size_t* written);
#ifdef __cplusplus
}
#endif
#endif /* _h_sra_illumina_ */
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