/usr/include/ncbi-vdb/align/reader-refseq.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 readten 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_align_reader_refseq_
#define _h_align_reader_refseq_
#ifndef _h_align_extern_
#include <align/extern.h>
#endif
#ifdef __cplusplus
extern "C" {
#endif
struct VDBManager;
struct VTable;
enum ETableReaderRefSeq_Options {
errefseq_4NA = 0x01 /* read in INSDC:4na:bin, INSDC:dna:text is default */
};
typedef struct TableReaderRefSeq TableReaderRefSeq;
ALIGN_EXTERN rc_t CC TableReaderRefSeq_MakeTable(const TableReaderRefSeq** cself, const struct VDBManager* vmgr,
const struct VTable* table, uint32_t options, size_t cache);
ALIGN_EXTERN rc_t CC TableReaderRefSeq_MakePath(const TableReaderRefSeq** cself, const VDBManager* vmgr,
const char* path, uint32_t options, size_t cache);
ALIGN_EXTERN void CC TableReaderRefSeq_Whack(const TableReaderRefSeq* cself);
ALIGN_EXTERN rc_t CC TableReaderRefSeq_SeqId(const TableReaderRefSeq* cself, const char** id, uint32_t* id_sz);
ALIGN_EXTERN rc_t CC TableReaderRefSeq_SeqLength(const TableReaderRefSeq* cself, INSDC_coord_len* len);
ALIGN_EXTERN rc_t CC TableReaderRefSeq_Circular(const TableReaderRefSeq* cself, bool* circular);
/* *md5 is NULL if not present */
ALIGN_EXTERN rc_t CC TableReaderRefSeq_MD5(const TableReaderRefSeq* cself, const uint8_t** md5);
/* read a chunk of refseq into buffer from offset up to offset + len
if offset is beyond non-circular refseq size error is returned
*/
ALIGN_EXTERN rc_t CC TableReaderRefSeq_Read(const TableReaderRefSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len,
uint8_t* buffer, INSDC_coord_len* written);
#ifdef __cplusplus
}
#endif
#endif /* _h_align_reader_refseq_ */
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