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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_map_file_
#define _h_sra_sort_map_file_
#ifndef _h_sra_sort_defs_
#include "sort-defs.h"
#endif
/*--------------------------------------------------------------------------
* forwards
*/
struct IdxMapping;
/*--------------------------------------------------------------------------
* MapFile
* a file for storing id mappings
*/
typedef struct MapFile MapFile;
/* Make
* creates an id map
*/
MapFile *MapFileMake ( const ctx_t *ctx, const char *name, bool random_access );
/* MakeForPoslen
* creates an id map with an additional poslen file
* this is specially for PRIMARY_ALIGNMENT_IDS and SECONDARY_ALIGNMENT_IDS
* that use *_ALIGNMENT global position and length as a sorting key
* we drop it to a file after its generation so that it can be
* picked up later when copying the corresponding alignment table.
*/
MapFile *MapFileMakeForPoslen ( const ctx_t *ctx, const char *name );
/* Release
*/
void MapFileRelease ( const MapFile *self, const ctx_t *ctx );
/* Duplicate
*/
MapFile *MapFileDuplicate ( const MapFile *self, const ctx_t *ctx );
/* SetIdRange
* required second-stage initialization
* must be called before any writes occur
*/
void MapFileSetIdRange ( MapFile *self, const ctx_t *ctx,
int64_t first_id, uint64_t num_ids );
/* First
* return first mapped id
* Count
* return number of ids
*/
int64_t MapFileFirst ( const MapFile *self, const ctx_t *ctx );
uint64_t MapFileCount ( const MapFile *self, const ctx_t *ctx );
/* SetOldToNew
* write new=>old id mappings
*/
void MapFileSetOldToNew ( MapFile *self, const ctx_t *ctx,
struct IdxMapping const *ids, size_t count );
/* SetNewToOld
* write new=>old id mappings
*/
void MapFileSetNewToOld ( MapFile *self, const ctx_t *ctx,
struct IdxMapping const *ids, size_t count );
/* SetPoslen
* write global position/length in new-id order
*/
void MapFileSetPoslen ( MapFile *self, const ctx_t *ctx,
struct IdxMapping const *ids, size_t count );
/* ReadPoslen
* read global position/length in new-id order
* starts reading at the indicated row
* returns the number read
*/
size_t MapFileReadPoslen ( const MapFile *self, const ctx_t *ctx,
int64_t start_id, uint64_t *poslen, size_t max_count );
/* AllocMissingNewIds
* it is possible to have written fewer new=>old mappings
* than are supposed to be there, e.g. SEQUENCE that gets
* initially written by align tables. unaligned sequences
* need to fill in the remainder.
*
* returns the first newly allocated id
*/
int64_t MapFileAllocMissingNewIds ( MapFile *self, const ctx_t *ctx );
/* SelectOldToNewPairs
* specify the range of new ids to select from
* read them in old=>new order
*/
size_t MapFileSelectOldToNewPairs ( const MapFile *self, const ctx_t *ctx,
int64_t start_id, struct IdxMapping *ids, size_t max_count );
/* SelectOldToNewSingle
* specify the range of new ids to select from
* read them in old=>new order
*/
size_t MapFileSelectOldToNewSingle ( const MapFile *self, const ctx_t *ctx,
int64_t start_id, int64_t *ids, uint32_t *opt_ord, size_t max_count );
/* MapSingleOldToNew
* reads a single old=>new mapping
* returns new id or 0 if not found
* optionally allocates a new id if "insert" is true
*/
int64_t MapFileMapSingleOldToNew ( MapFile *self, const ctx_t *ctx,
int64_t old_id, bool insert );
/* MapMultipleOldToNew
* reads a single old=>new mapping
* returns new id or 0 if not found
* optionally allocates a new id if "insert" is true
*/
void MapFileMapMultipleOldToNew ( MapFile *self, const ctx_t *ctx,
int64_t *ids, size_t count, bool insert );
/* ConsistencyCheck
* should be const, but MapFileOldToNew claims to be non-const
* and is used within. only non-const if "insert" is true.
*/
void MapFileConsistencyCheck ( const MapFile *self, const ctx_t *ctx );
#endif
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