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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_sra_sort_
#define _h_sra_sort_
#ifndef _h_sra_sort_defs_
#include "sort-defs.h"
#endif
#ifndef _h_kfs_defs_
#include <kfs/defs.h>
#endif
#ifndef _h_kdb_column_
#include <kdb/column.h>
#endif
#define NEW_TYPES 1
/*--------------------------------------------------------------------------
* forwards
*/
struct DbPair;
struct TablePair;
/*--------------------------------------------------------------------------
* Selection
* input selection criteria
*/
typedef struct Selection Selection;
struct Selection
{
int dummy;
};
/*--------------------------------------------------------------------------
* Tool
* parameter block generated by KMain
*/
typedef struct Tool Tool;
struct Tool
{
/* input selection */
const Selection *sel;
/* directory for temporary files */
const char *tmpdir;
/* directory for mmap page files */
const char *mmapdir;
/* source object path */
const char *src_path;
/* destination object path */
const char *dst_path;
/* buffer size for id map files */
size_t map_file_bsize;
size_t map_file_random_bsize;
/* the number of ids to gather at a time */
size_t max_ref_idx_ids;
size_t max_large_idx_ids;
size_t max_poslen_ids;
size_t max_idx_ids;
size_t min_idx_ids;
/* the number of missing SEQUENCE ids to gather at a time */
size_t max_missing_ids;
/* pid of tool */
int pid;
/* db create mode */
struct
{
KCreateMode cmode;
} db;
/* tbl create mode */
struct
{
KCreateMode cmode;
} tbl;
/* column blob checksum mode */
struct
{
size_t pgsize;
KCreateMode cmode;
KChecksum checksum;
} col;
/* ignore failure on multiple sorts */
bool ignore;
/* force overwrite */
bool force;
/* write new=>old mappings
not normally needed */
bool write_new_to_old;
/* whether to apply a sort on old-id
before writing old=>new mapping or
to let pagefile handle it */
bool sort_before_old2new;
/* normally remove idx files right away
but if they are being debugged... */
bool unlink_idx_files;
/* perform consistency check on index */
bool idx_consistency_check;
};
/*--------------------------------------------------------------------------
* TypeParams
* object type params
*/
typedef struct TypeParams TypeParams;
struct TypeParams
{
char src_type [ 256 ];
char dst_type [ 256 ];
char view_type [ 256 ];
};
/*--------------------------------------------------------------------------
* sra-sort functions
*/
/* run
* called from KMain
* determines the type of object being copied/sorted
* opens input object
* dispatches to the appropriate handler
*/
void run ( const ctx_t *ctx );
rc_t copy_stats_metadata( const char * src_path, const char * dst_path );
#endif
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