/usr/include/ncbi-vdb/insdc/sra.h is in libncbi-vdb-dev 2.8.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
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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_insdc_sra_
#define _h_insdc_sra_
#ifndef _h_insdc_insdc_
#include <insdc/insdc.h>
#endif
#ifdef __cplusplus
extern "C" {
#endif
/*==========================================================================
* INSDC SRA types, constants
*/
/* spotid_t
* unique id given to every spot
*/
typedef int64_t INSDC_SRA_spotid_t;
/* spot_ids_found
* returns a tuple of spot ids
*/
typedef uint64_t INSDC_SRA_spot_ids_found [ 4 ];
/* read filter
*/
#define sra_read_filter_t "INSDC:SRA:read_filter"
typedef INSDC_read_filter INSDC_SRA_read_filter;
enum
{
SRA_READ_FILTER_PASS = READ_FILTER_PASS,
SRA_READ_FILTER_REJECT = READ_FILTER_REJECT,
SRA_READ_FILTER_CRITERIA = READ_FILTER_CRITERIA,
SRA_READ_FILTER_REDACTED = READ_FILTER_REDACTED
};
/* read type
* describes the type of read within a spot
* the extended version also describes its orientation
*/
#define sra_read_type_t "INSDC:SRA:xread_type"
typedef INSDC_read_type INSDC_SRA_xread_type;
typedef INSDC_SRA_xread_type INSDC_SRA_read_type;
enum
{
/* read_type and xread_type */
SRA_READ_TYPE_TECHNICAL = READ_TYPE_TECHNICAL,
SRA_READ_TYPE_BIOLOGICAL = READ_TYPE_BIOLOGICAL,
/* xread_type only - applied as bits, e.g.:
type = SRA_READ_TYPE_BIOLOGICAL | SRA_READ_TYPE_REVERSE */
SRA_READ_TYPE_FORWARD = READ_TYPE_FORWARD,
SRA_READ_TYPE_REVERSE = READ_TYPE_REVERSE
};
/* platform id
*/
#define sra_platform_id_t "INSDC:SRA:platform_id"
typedef uint8_t INSDC_SRA_platform_id;
enum
{
SRA_PLATFORM_UNDEFINED = 0,
SRA_PLATFORM_454 = 1,
SRA_PLATFORM_ILLUMINA = 2,
SRA_PLATFORM_ABSOLID = 3,
SRA_PLATFORM_COMPLETE_GENOMICS = 4,
SRA_PLATFORM_HELICOS = 5,
SRA_PLATFORM_PACBIO_SMRT = 6,
SRA_PLATFORM_ION_TORRENT = 7,
SRA_PLATFORM_CAPILLARY = 8,
SRA_PLATFORM_OXFORD_NANOPORE = 9
};
#ifdef __cplusplus
}
#endif
#endif /* _h_insdc_sra_ */
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