/usr/include/ncbi-vdb/loader/reference-writer.h is in libncbi-vdb-dev 2.8.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
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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 LOADER_REFERENCE_WRITER_H_
#define LOADER_REFERENCE_WRITER_H_ 1
#include <vdb/manager.h>
#include <vdb/database.h>
#include <vdb/table.h>
#include <klib/data-buffer.h>
#include <align/writer-reference.h>
#include "alignment-writer.h"
typedef struct Reference {
const ReferenceMgr *mgr;
const ReferenceSeq *rseq;
int64_t lastRefId;
int32_t lastOffset;
unsigned curPos;
unsigned endPos;
unsigned length;
KDataBuffer coverage;
KDataBuffer mismatches;
KDataBuffer indels;
KDataBuffer pri_align;
KDataBuffer sec_align;
KDataBuffer pri_overlap;
KDataBuffer sec_overlap;
bool out_of_order;
bool acceptHardClip;
char last_id[256];
} Reference;
rc_t ReferenceInit(Reference *self, const VDBManager *mgr, VDatabase *db,
bool expectUnsorted,
bool acceptHardClip,
char const *refXRefPath,
char const *inpath,
uint32_t maxSeqLen, /*TODO: save in Reference object, reuse in other functions*/
char const** refFiles
);
rc_t ReferenceSetFile(Reference *self, const char *id, uint64_t length, uint8_t const md5[16], uint32_t maxSeqLen, bool *shouldUnmap);
rc_t ReferenceVerify(Reference const *self, char const id[], uint64_t length, uint8_t const md5[16]);
rc_t ReferenceGet1stRow(Reference const *self, int64_t *refID, char const refName[]);
rc_t ReferenceAddAlignId(Reference *self,
int64_t align_id,
bool is_primary
);
rc_t ReferenceRead(Reference *self, AlignmentRecord *data, uint64_t const pos,
uint32_t const rawCigar[], uint32_t const cigCount,
char const seqDNA[], uint32_t const seqLen,
uint8_t rna_orient, uint32_t *matches,
bool acceptNoMatch, unsigned minMatchCount, uint32_t maxSeqLen);
rc_t ReferenceWhack(Reference *self, bool commit, uint32_t maxSeqLen, rc_t (*const quitting)(void));
#endif
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