/usr/include/ncbi-vdb/sra/sff.h is in libncbi-vdb-dev 2.8.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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_sff_
#define _h_sra_sff_
#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
/*--------------------------------------------------------------------------
* SFFReader
*/
typedef struct SFFReader SFFReader;
/* Make
* create SFFReader reference based
* on table and properties:
* table - SRATable
* accession - accession
* 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 SFFReaderMake(const SFFReader** self, const SRATable* table, const char* accession,
spotid_t minSpotId, spotid_t maxSpotId);
/* Whack
* releases object obtained from SFFReaderMake
*/
SRA_RD_EXTERN rc_t CC SFFReaderWhack(const SFFReader* self);
/* FirstSpot
* set current spot to first in the run
*/
SRA_RD_EXTERN rc_t CC SFFReaderFirstSpot(const SFFReader* self);
/* SeekSpot
* set current spot
* if error occurred current spot position becomes 0
*/
SRA_RD_EXTERN rc_t CC SFFReaderSeekSpot(const SFFReader* self, spotid_t spot);
/* NextSpot
* Seek to next spot from current
*/
SRA_RD_EXTERN rc_t CC SFFReaderNextSpot(const SFFReader* 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 SFFReaderCurrentSpot(const SFFReader* 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 SFFReader_SpotInfo(const SFFReader* 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_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 SFFReader_SpotReadInfo(const SFFReader* 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);
/* Header
* retrieve binary file header
* spots [IN,OPT] - sets number of reads in header, ignored if spots == 0
* data [IN] - pointer to buffer for printing
* dsize [IN] - data buffer size
* written [IN,OUT] - number of bytes occupied by data, may by more than dsize
*/
SRA_RD_EXTERN rc_t CC SFFReaderHeader(const SFFReader* self, spotid_t spots, char* data, size_t dsize, size_t* written);
/* Base
* retrieve bases for the spot
* other parameters see description for SFFReaderHeader above
*/
SRA_RD_EXTERN rc_t CC SFFReaderReadHeader(const SFFReader* self, char* data, size_t dsize, size_t* written);
/* QualityName
* retrieve quality name string for the spot
* other parameters see description for SFFReaderHeader above
*/
SRA_RD_EXTERN rc_t CC SFFReaderReadData(const SFFReader* self, char* data, size_t dsize, size_t* written);
/* GetCurrentSpotData
* retrieve current spot data as a blob
* other parameters see description for SFFReaderHeader above
*/
SRA_RD_EXTERN rc_t CC SFFReader_GetCurrentSpotData(const SFFReader* 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
* other parameters see description for SFFReaderHeader above
*/
SRA_RD_EXTERN rc_t CC SFFReader_GetNextSpotData(const SFFReader* self, char* data, size_t dsize, size_t* written);
#ifdef __cplusplus
}
#endif
#endif /* _h_sra_sff_ */
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