/usr/include/ncbi-vdb/ncbi/spotname.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_ncbi_spotname_
#define _h_ncbi_spotname_
#ifndef _h_klib_defs_
#include <klib/defs.h>
#endif
#ifdef __cplusplus
extern "C" {
#endif
/*==========================================================================
* NCBI Sequence Read Archive schema
*/
/*--------------------------------------------------------------------------
* types
*/
/* spot_name_token
* a vector describing tokens recognized within a spot name
*
* COMPONENTS:
* 0 - token id
* 1 - token starting coordinate
* 2 - token length
*/
typedef uint16_t NCBI_SRA_spot_name_token [ 3 ];
/* token values
*
* tokens are produced by a schema-specific tokenizer function
* this function is purposely abstract because it may rely upon
* whatever information it needs to perform its task. the only
* requirement is that it produce these tokens as its output.
*
* an empty name input must produce no tokens. in this case,
* there is no name to tokenize or data to produce.
*
* a non-empty name must produce 1 or more tokens of output.
* all tokens must be ordered by starting character position.
*
* if a name does not conform to any pattern recognized by the
* tokenizer, then the tokenizer emits a single token of "unrecognized"
*
* if a name conforms to some pattern but does not have any
* substitution tokens, the tokenizer emits a single token of "recognized"
*
* if a name may be tokenized, then the resulting tokens should
* describe only the portions of the string that should be removed
* from the name, e.g. "X" or "Y".
*
* the standard coordinates "X".."L" are given in unsigned decimal.
* alternate representations are contained within their respective
* namespaces: "signed", "hex" and "octal".
*
* the special coordinate "Q" represents the 454-specific encoding
* of X and Y into base-36, where the formula for Q is:
* Q = 4096 * X + Y
* and ASCII encoding:
* 0..25 => "A-Z", 26..35 => "0-9"
*/
enum
{
NCBI_SRA_name_token_unrecognized = 1,
NCBI_SRA_name_token_recognized = 2,
NCBI_SRA_name_token_Q = 3,
NCBI_SRA_name_token_X = 4,
NCBI_SRA_name_token_Y = 5,
NCBI_SRA_name_token_T = 6,
NCBI_SRA_name_token_L = 7,
NCBI_SRA_name_token_signed_X = 8,
NCBI_SRA_name_token_signed_Y = 9,
NCBI_SRA_name_token_signed_T = 10,
NCBI_SRA_name_token_signed_L = 11,
NCBI_SRA_name_token_octal_X = 12,
NCBI_SRA_name_token_octal_Y = 13,
NCBI_SRA_name_token_octal_T = 14,
NCBI_SRA_name_token_octal_L = 15,
NCBI_SRA_name_token_hex_upper_X = 16,
NCBI_SRA_name_token_hex_upper_Y = 17,
NCBI_SRA_name_token_hex_upper_T = 18,
NCBI_SRA_name_token_hex_upper_L = 19,
NCBI_SRA_name_token_hex_lower_X = 20,
NCBI_SRA_name_token_hex_lower_Y = 21,
NCBI_SRA_name_token_hex_lower_T = 22,
NCBI_SRA_name_token_hex_lower_L = 23
};
/* token symbols
* when a name matches some pattern and tokens are recognized,
* the tokens are extracted from the name and sent to individual
* columns, and replaced with the symbols below to create a
* formatted name.
*/
enum
{
NCBI_SRA_name_symbol_Q = 'Q',
NCBI_SRA_name_symbol_X = 'X',
NCBI_SRA_name_symbol_Y = 'Y',
NCBI_SRA_name_symbol_T = 'T',
NCBI_SRA_name_symbol_L = 'L',
NCBI_SRA_name_symbol_octal_X = 'a',
NCBI_SRA_name_symbol_octal_Y = 'b',
NCBI_SRA_name_symbol_octal_T = 'c',
NCBI_SRA_name_symbol_octal_L = 'd',
NCBI_SRA_name_symbol_hex_upper_X = 'e',
NCBI_SRA_name_symbol_hex_upper_Y = 'f',
NCBI_SRA_name_symbol_hex_upper_T = 'g',
NCBI_SRA_name_symbol_hex_upper_L = 'h',
NCBI_SRA_name_symbol_hex_lower_X = 'x',
NCBI_SRA_name_symbol_hex_lower_Y = 'y',
NCBI_SRA_name_symbol_hex_lower_T = 't',
NCBI_SRA_name_symbol_hex_lower_L = 'l'
};
#ifdef __cplusplus
}
#endif
#endif /* _h_ncbi_spotname_ */
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