/usr/include/ncbi-vdb/align/writer-reference.h is in libncbi-vdb-dev 2.8.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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_align_writer_reference_
#define _h_align_writer_reference_
#ifndef _h_align_extern_
#include <align/extern.h>
#endif
#include <insdc/insdc.h>
#include <align/writer-cmn.h>
#include <align/writer-alignment.h>
#include <align/reader-refseq.h>
#ifdef __cplusplus
extern "C" {
#endif
struct KFile;
enum EReference_Options {
ewrefmgr_co_allREADs = 0x01, /* always write READ */
ewrefmgr_co_Coverage = 0x02, /* use coverage data, by default not used */
ewrefmgr_co_AcceptHardClip = 0x04 /* accept hard clipping in CIGAR */
};
typedef struct ReferenceMgr ReferenceMgr;
/* Writes REFERENCE table with in given db
vmgr [IN] - needed only if conf is not NULL
conf [IN] - optional path to tab separated file to resolve reference names
from source files to standard refseq accessions;
standard refseq dictionary location is obtained from kfg files.
path {IN] - optional path points to a directory with 'local' references
(not found in conf file), default is '.'
max_seq_len [IN] - 0 - use default
cache [IN] - db cache size per single!!! reference (vdb cursor cache)
num_open [IN] - number of refseq kept open, 0 - no limit
*/
ALIGN_EXTERN rc_t CC ReferenceMgr_Make(const ReferenceMgr** cself, VDatabase* db, const VDBManager* vmgr,
const uint32_t options, const char* conf, const char* path, uint32_t max_seq_len,
size_t cache, uint32_t num_open);
ALIGN_EXTERN rc_t CC ReferenceMgr_Release(const ReferenceMgr *cself,
const bool commit,
uint64_t *const Rows,
const bool build_coverage,
rc_t (*const quitting)(void)
);
ALIGN_EXTERN rc_t CC ReferenceMgr_SetCache(ReferenceMgr const *const self, size_t cache, uint32_t num_open);
typedef struct ReferenceSeq ReferenceSeq;
/* id: chr12 or NC_000001.3 */
ALIGN_EXTERN rc_t CC ReferenceMgr_GetSeq(ReferenceMgr const *self,
ReferenceSeq const **seq,
char const id[],
bool *shouldUnmap,
bool allowMultiMapping,
bool wasRenamed[]);
ALIGN_EXTERN rc_t CC ReferenceMgr_Verify(ReferenceMgr const *self,
char const id[],
INSDC_coord_len length,
uint8_t const md5[16],
bool allowMultiMapping,
bool wasRenamed[]);
ALIGN_EXTERN rc_t CC ReferenceMgr_FastaPath(const ReferenceMgr* cself, const char* fasta_path);
ALIGN_EXTERN rc_t CC ReferenceMgr_FastaFile(const ReferenceMgr* cself, struct KFile const* file);
enum EReference_CompressionOptions {
ewrefmgr_cmp_Binary = 0x01, /* binary cigar on input (BAM format: 28+4 bits) */
ewrefmgr_cmp_Exact = 0x02 /* exact matching no cliping */
};
ALIGN_EXTERN rc_t CC ReferenceMgr_Compress(const ReferenceMgr* cself,
uint32_t options,
const char* id,
INSDC_coord_zero offset,
const char* seq,
INSDC_coord_len seq_len,
const void* cigar,
uint32_t cigar_len,
INSDC_coord_zero allele_offset,
const char* allele,
INSDC_coord_len allele_len,
INSDC_coord_zero offset_in_allele,
const void* allele_cigar,
uint32_t allele_cigar_len,
uint8_t rna_orient,
TableWriterAlgnData* data);
/* Read refseq chunk of 'len' bases into provided 'buffer' (must be enough big for len);
ref_len - on return has number of bases written to the buffer
*/
ALIGN_EXTERN rc_t CC ReferenceSeq_Read(const ReferenceSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len,
uint8_t* buffer, INSDC_coord_len* ref_len);
ALIGN_EXTERN rc_t CC ReferenceSeq_Get1stRow(const ReferenceSeq* cself, int64_t* row_id);
ALIGN_EXTERN rc_t CC ReferenceSeq_GetID(ReferenceSeq const *self, char const **rslt);
ALIGN_EXTERN rc_t CC ReferenceSeq_Compress(const ReferenceSeq* cself,
uint32_t options,
INSDC_coord_zero offset,
const char* seq,
INSDC_coord_len seq_len,
const void* cigar,
uint32_t cigar_len,
INSDC_coord_zero allele_offset,
const char* allele,
INSDC_coord_len allele_len,
INSDC_coord_zero offset_in_allele,
const void* allele_cigar,
uint32_t allele_cigar_len,
uint8_t rna_orient,
TableWriterAlgnData* data);
ALIGN_EXTERN rc_t CC ReferenceSeq_TranslateOffset_int(ReferenceSeq const *const cself,
INSDC_coord_zero const offset,
int64_t *const ref_id,
INSDC_coord_zero *const ref_start,
uint64_t *const global_ref_start);
enum ReferenceSeqCoverageTableType {
ewrefcov_primary_table = 0,
ewrefcov_secondary_table,
ewrefcov_evidence_table
};
typedef struct ReferenceSeqCoverage_struct {
/* based only on primary and secondary */
uint8_t high;
uint8_t low;
uint32_t mismatches;
uint32_t indels;
/* in that order (use enum above): prim, 2nd, evidence */
INSDC_coord_zero overlap_ref_pos[3];
INSDC_coord_len overlap_ref_len[3];
TableWriterData ids[3];
} ReferenceSeqCoverage;
ALIGN_EXTERN rc_t CC ReferenceSeq_AddCoverage(const ReferenceSeq* cself, INSDC_coord_zero offset, const ReferenceSeqCoverage* data);
ALIGN_EXTERN rc_t CC ReferenceSeq_Release(const ReferenceSeq* cself);
#ifdef __cplusplus
}
#endif
#endif /* _h_align_writer_reference_ */
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