/usr/include/ncbi-vdb/sra/sff-file.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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 | /*===========================================================================
*
* 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_file_
#define _h_sra_sff_file_
#include <klib/defs.h>
#ifdef __cplusplus
extern "C" {
#endif
/* ======================================================================
* SFF defines an 8 bit value in the file that tells of the format of the
* data signal (flowgrams in Roche 454 SFF parlance).
*
* The only currently defined format is a 16 bit unsigned integer in
* units one hundredths. This enum is to easily allow us to add other
* formats if ever required.
*/
typedef enum SFFFormatCode
{
SFFFormatCodeUnset = 0,
/* values are 16 integers of hundreths of units: 0 = 0.00, 1 = 0.01, 2 = 0.02, ... */
SFFFormatCodeUI16Hundreths,
/* currently (SFF (00000001) yet this is the only one SFFFormatCode is defined */
SFFFormatCodeUndefined
} SFFFormatCode;
/* ----------------------------------------------------------------------
* Common Header Section
* (Genome Sequencer Data Analysis Software Manual Section 13.3.8.1)
*/
#define SFFCommonHeader_size 31
typedef struct SFFCommonHeader_struct
{
uint32_t magic_number; /* four bytes ".sff" as string: with wrong endian it would be "ffs." */
uint32_t version; /* four bytes 0x00000001 */
uint64_t index_offset; /* index_offset and index_length are the offset and length of an */
uint32_t index_length; /* optional index of the reads in the file. If no index both are 0 */
uint32_t number_of_reads; /* The number of reads in the file (not individual datum) */
uint16_t header_length; /* length of all headers in this set. 31 + flow_length + key_length + pad to 8 byte boundary */
uint16_t key_length; /* length of the key sequence for these reads */
uint16_t num_flows_per_read; /* the number of flows for each read in this file */
uint8_t flowgram_format_code; /* SFFFormatCode between (SFFFormatCodeUnset..FormateCodeUndefined) exclusive */
/* not included variable length portion of header:
flow chars - sequence of uint8_t, actual length is num_flows_per_read above
key sequence - sequence of uint8_t, actual length is key_length above
padding - sequence of zeroed uint8_t to make total length of file header 8-byte padded
*/
} SFFCommonHeader;
/* ----------------------------------------------------------------------
* Read Header Section
* (Genome Sequencer Data Analysis Software Manual Section 13.3.8.2)
*/
#define SFFReadHeader_size 16
typedef struct SFFReadHeader_struct
{
uint16_t header_length; /* length in bytes of the full section including padding */
uint16_t name_length; /* length of the name of this spot */
uint32_t number_of_bases;
uint16_t clip_quality_left;
uint16_t clip_quality_right;
uint16_t clip_adapter_left;
uint16_t clip_adapter_right;
/* not included variable length portion of header:
name - sequence of uint8_t, actual length is name_length above
padding - sequence of zeroed uint8_t to make total length of read header 8-byte padded
read data section:
signal - sequence of uint16_t (if flowgram_format_code == SFFFormatCodeUI16Hundreths, see enum above),
actual length is num_flows_per_read from file header above
flow_index_per_base (position) - sequence of uint8_t, actual length in number_of_bases above
bases - sequence of uint8_t, actual length in number_of_bases above
quality_scores - sequence of uint8_t, actual length in number_of_bases above
padding - sequence of zeroed uint8_t to make total length of read data section 8-byte padded
*/
} SFFReadHeader;
#ifdef __cplusplus
}
#endif
#endif /* _h_sra_sff_file_ */
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