/usr/include/ncbi-vdb/align/writer-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 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_align_writer_refseq_
#define _h_align_writer_refseq_
#ifndef _h_align_extern_
#include <align/extern.h>
#endif
#include <vdb/manager.h>
#include <align/writer-cmn.h>
#ifdef __cplusplus
extern "C" {
#endif
/* default sequence chunk length */
#define TableWriterRefSeq_MAX_SEQ_LEN 5000
/* use in TableWriterRefSeq_Write* methods */
enum ETableWriterRefSeq_ColNames {
ewrefseq_cn_MAX_SEQ_LEN, /* static/default */
ewrefseq_cn_DEF_LINE, /* static/default */
ewrefseq_cn_CS_KEY, /* handled by writer */
ewrefseq_cn_READ,
ewrefseq_cn_QUALITY, /* optional */
ewrefseq_cn_SEQ_ID, /* static/default */
ewrefseq_cn_SEQ_START, /* calculated on fly by writer */
ewrefseq_cn_SEQ_LEN, /* calculated on fly by writer */
ewrefseq_cn_CIRCULAR, /* static/default */
ewrefseq_cn_Last = ewrefseq_cn_CIRCULAR
};
enum ETableWriterRefSeq_ColOptions {
ewrefseq_co_QUALITY = 0x01 /* use QUALITY column, by default not opened */
};
typedef struct TableWriterRefSeqData_struct {
TableWriterData read;
TableWriterData quality;
} TableWriterRefSeqData;
typedef struct TableWriterRefSeq TableWriterRefSeq;
ALIGN_EXTERN rc_t CC TableWriterRefSeq_Make(const TableWriterRefSeq** cself, VDBManager* mgr, const char* schema_path,
const char* table_path, const uint32_t options);
/* rows optional here, app signature is mandatory */
ALIGN_EXTERN rc_t CC TableWriterRefSeq_Whack(const TableWriterRefSeq* cself, bool commit, uint64_t* rows,
const char loader_name[],
const ver_t loader_version,
const char loader_date[],
const char app_name[],
const ver_t app_version);
ALIGN_EXTERN rc_t CC TableWriterRefSeq_WriteDefault(const TableWriterRefSeq* cself,
enum ETableWriterRefSeq_ColNames col, const TableWriterData* data);
/* rowid optional here */
ALIGN_EXTERN rc_t CC TableWriterRefSeq_Write(const TableWriterRefSeq* cself, const TableWriterRefSeqData* data, int64_t* rowid);
#ifdef __cplusplus
}
#endif
#endif /* _h_align_writer_refseq_ */
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