/usr/include/ncbi-vdb/align/refseq-mgr.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_refseq_mgr_
#define _h_align_refseq_mgr_
#ifndef _h_align_extern_
#include <align/extern.h>
#endif
#include <vdb/manager.h>
#include <vdb/table.h>
#include <align/reader-refseq.h>
#ifdef __cplusplus
extern "C" {
#endif
typedef struct RefSeqMgr RefSeqMgr;
/* Manages refseq tables
reader_options [IN] - passed to TableReaderRefSeq
cache [IN] - db cache size per single!!! reference (vdb cursor cache)
keep_open_num [IN] - number of refseq kept open, 0 - no limit
*/
ALIGN_EXTERN rc_t CC RefSeqMgr_Make(const RefSeqMgr** cself, const VDBManager* vmgr,
uint32_t reader_options, size_t cache, uint32_t keep_open_num);
ALIGN_EXTERN rc_t CC RefSeqMgr_Release(const RefSeqMgr* cself);
ALIGN_EXTERN rc_t CC RefSeqMgr_SetCache(RefSeqMgr const *const cself, size_t cache, uint32_t keep_open_num);
/* return value if 0 means object was found, path is optional */
ALIGN_EXTERN rc_t RefSeqMgr_Exists(const RefSeqMgr* cself, const char* accession, uint32_t accession_sz, char** path);
/* Read from refseq ided by seq_id chunk of 'len' bases into provided 'buffer' (must be enough big for len);
on return written has number of bases written
*/
ALIGN_EXTERN rc_t CC RefSeqMgr_Read(const RefSeqMgr* cself, const char* seq_id, uint32_t seq_id_sz,
INSDC_coord_zero offset, INSDC_coord_len len,
uint8_t* buffer, INSDC_coord_len* written);
typedef struct RefSeq RefSeq;
ALIGN_EXTERN rc_t CC RefSeqMgr_GetSeq(const RefSeqMgr* cmgr, const RefSeq** cself, const char* seq_id, uint32_t seq_id_sz);
/* Same as RefSeqMgr_Read
*/
ALIGN_EXTERN rc_t CC RefSeq_Read(const RefSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len,
uint8_t* buffer, INSDC_coord_len* written);
ALIGN_EXTERN rc_t CC RefSeq_Circular(const RefSeq* cself, bool* circular);
ALIGN_EXTERN rc_t CC RefSeq_SeqLength(const RefSeq* cself, INSDC_coord_len* len);
ALIGN_EXTERN rc_t CC RefSeq_MD5(const RefSeq* cself, const uint8_t** md5);
ALIGN_EXTERN rc_t CC RefSeq_Name(const RefSeq* cself, const char** name);
ALIGN_EXTERN rc_t CC RefSeq_Release(const RefSeq* cself);
#ifdef __cplusplus
}
#endif
#endif /* _h_align_refseq_mgr_ */
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