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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_csra_pair_
#define _h_sra_sort_csra_pair_
#ifndef _h_sra_sort_db_pair_
#include "db-pair.h"
#endif
#ifndef SEQUENCE_BEFORE_SECONDARY
#define SEQUENCE_BEFORE_SECONDARY 1
#endif
/*--------------------------------------------------------------------------
* forwards
*/
struct TablePair;
struct ColumnWriter;
/*--------------------------------------------------------------------------
* cSRAPair
* interface to pairing of source and destination tables
*/
typedef struct cSRAPair cSRAPair;
struct cSRAPair
{
DbPair dad;
/* for ultimate metadata */
int64_t first_half_aligned_spot;
int64_t first_unaligned_spot;
/* the reference table */
struct TablePair *reference;
/* the alignment tables */
struct TablePair *prim_align, *sec_align, *evidence_align;
/* the sequence table */
struct TablePair *sequence;
/* mapping indices */
struct MapFile *pa_idx, *sa_idx, *seq_idx;
};
/* Make
* makes an object based upon open source and destination VDatabase objects
*/
DbPair *cSRAPairMake ( const ctx_t *ctx,
struct VDatabase const *src, struct VDatabase *dst, const char *name );
/* MakeFirstHalfAlignedRowIdCaptureWriter
* a simple monitor on SEQUENCE.PRIMARY_ALIGNMENT_ID looking for
* half-aligned spots and capturing the first occurrence.
*/
struct ColumnWriter *cSRAPairMakeFirstHalfAlignedRowIdCaptureWriter ( cSRAPair *self,
const ctx_t *ctx, struct ColumnWriter *writer );
#endif /* _h_sra_sort_csra_pair_ */
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