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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 BAM_LOAD_ALIGNMENT_WRITER_H_
#define BAM_LOAD_ALIGNMENT_WRITER_H_ 1
#include <klib/data-buffer.h>
#include <vdb/database.h>
#include <vdb/table.h>
#include <vdb/cursor.h>
#include <insdc/insdc.h>
#include <align/writer-alignment.h>
typedef struct s_alignment Alignment;
typedef struct AlignmentRecord AlignmentRecord;
struct AlignmentRecord {
KDataBuffer buffer;
TableWriterAlgnData data;
int64_t alignId;
bool isPrimary;
INSDC_coord_one read_id;
int64_t ref_id;
INSDC_coord_zero ref_start;
uint64_t global_ref_start;
bool ref_orientation;
uint32_t mapq;
uint64_t tmp_key_id;
INSDC_coord_zero read_start;
INSDC_coord_len read_len;
bool mate_ref_orientation;
int64_t mate_ref_id;
INSDC_coord_zero mate_ref_pos;
int64_t mate_align_id;
int32_t template_len;
};
#define AR_REF_ID(X) ((X).ref_id)
#define AR_REF_START(X) ((X).global_ref_start)
#define AR_REF_LEN(X) ((X).ref_len)
#define AR_REF_ORIENT(X) ((X).ref_orientation)
#define AR_READNO(X) ((X).read_id)
#define AR_MAPQ(X) ((X).mapq)
#define AR_KEY(X) ((X).tmp_key_id)
#define AR_BASECOUNT(X) ((X).data.has_mismatch.elements)
#define AR_HAS_MISMATCH(X) ((bool *)((X).data.has_mismatch.buffer))
#define AR_HAS_OFFSET(X) ((bool *)((X).data.has_ref_offset.buffer))
#define AR_NUM_MISMATCH(X) ((X).data.mismatch.elements)
#define AR_MISMATCH(X) ((char *)((X).data.mismatch.buffer))
#define AR_NUM_OFFSET(X) ((X).data.ref_offset.elements)
#define AR_OFFSET(X) ((INSDC_coord_zero *)((X).data.ref_offset.buffer))
#define AR_OFFSET_TYPE(X) ((uint8_t *)((X).data.ref_offset_type.buffer))
#define AR_LINKAGE_GROUP(X) ((X).data.linkageGroup)
Alignment *AlignmentMake(VDatabase *db);
rc_t AlignmentWriteRecord(Alignment *self, AlignmentRecord *data);
rc_t AlignmentStartUpdatingSpotIds(Alignment *self);
rc_t AlignmentGetSpotKey(Alignment *self, uint64_t *keyId);
rc_t AlignmentWriteSpotId(Alignment *self, int64_t spotId);
rc_t AlignmentWhack(Alignment *self, bool commit);
rc_t AlignmentRecordInit(AlignmentRecord *self, unsigned readlen);
#endif
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