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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_SEQUENCE_WRITER_H_
#define BAM_LOAD_SEQUENCE_WRITER_H_ 1
#include <vdb/manager.h>
#include <vdb/database.h>
#include <vdb/table.h>
#include <vdb/cursor.h>
#include <klib/text.h>
#include <klib/data-buffer.h>
struct TableWriterSeq;
typedef struct s_sequence_record {
char *seq;
uint8_t *qual;
uint32_t *readStart;
uint32_t *readLen;
uint8_t *orientation;
uint8_t *is_bad;
uint8_t *alignmentCount;
char const *spotGroup;
char const *linkageGroup;
bool *aligned;
char *cskey;
uint64_t *ti;
uint64_t keyId;
unsigned spotGroupLen;
unsigned linkageGroupLen;
unsigned numreads;
} SequenceRecord;
typedef struct s_sequence_record_storage {
uint64_t ti[2];
uint32_t readStart[2];
uint32_t readLen[2];
uint8_t orientation[2];
uint8_t is_bad[2];
uint8_t alignmentCount[2];
bool aligned[2];
char cskey[2];
} SequenceRecordStorage;
typedef struct s_sequence {
VDatabase *db;
struct TableWriterSeq const *tbl;
} Sequence;
Sequence *SequenceInit(Sequence *self, VDatabase *db);
rc_t SequenceWriteRecord(Sequence *self, SequenceRecord const *rec,
bool color, bool isDup, INSDC_SRA_platform_id platform);
rc_t SequenceDoneWriting(Sequence *self);
rc_t SequenceReadKey(const Sequence *self, int64_t row, uint64_t *key);
rc_t SequenceUpdateAlignData(Sequence *self, int64_t row, unsigned nreads,
const int64_t primeId[/* nreads */],
const uint8_t alignCount[/* nreads */]);
void SequenceWhack(Sequence *self, bool commit);
#endif /* ndef BAM_LOAD_SEQUENCE_WRITER_H_ */
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