/usr/include/ncbi-vdb/align/writer-alignment.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_alignment_
#define _h_align_writer_alignment_
#ifndef _h_align_extern_
#include <align/extern.h>
#endif
#include <align/writer-cmn.h>
#ifdef __cplusplus
extern "C" {
#endif
enum ETableWriterAlgn_ColNames {
ewalgn_cn_TMP_KEY_ID,
ewalgn_cn_PLOIDY,
ewalgn_cn_SEQ_SPOT_ID,
ewalgn_cn_SEQ_READ_ID,
ewalgn_cn_READ_START,
ewalgn_cn_READ_LEN,
ewalgn_cn_REF_ID,
ewalgn_cn_REF_START,
ewalgn_cn_GLOBAL_REF_START,
ewalgn_cn_REF_LEN,
ewalgn_cn_REF_ORIENTATION,
ewalgn_cn_REF_PLOIDY,
ewalgn_cn_MATE_REF_ORIENTATION,
ewalgn_cn_MATE_REF_ID,
ewalgn_cn_MATE_REF_POS,
ewalgn_cn_MATE_ALIGN_ID,
ewalgn_cn_TEMPLATE_LEN,
ewalgn_cn_MAPQ,
ewalgn_cn_HAS_MISMATCH,
ewalgn_cn_HAS_REF_OFFSET,
ewalgn_cn_MISMATCH,
ewalgn_cn_REF_OFFSET,
ewalgn_cn_REF_OFFSET_TYPE,
ewalgn_cn_EVIDENCE_ALIGNMENT_IDS,
ewalgn_cn_ALIGN_GROUP,
ewalgn_cn_LINKAGE_GROUP,
ewalgn_cn_MISMATCH_QUALITY,
ewalgn_cn_MATE_GLOBAL_REF_START,
ewalgn_cn_MATE_REF_START,
ewalgn_cn_Last
};
typedef uint8_t ETableWriterAlgn_TableType;
enum {
ewalgn_tabletype_PrimaryAlignment,
ewalgn_tabletype_SecondaryAlignment,
ewalgn_tabletype_EvidenceInterval,
ewalgn_tabletype_EvidenceAlignment
};
enum ETableWriterAlgn_ColOptions {
ewalgn_co_SEQ_SPOT_ID = 0x01, /* SEQ_SPOT_ID will be written with the whole record */
ewalgn_co_TMP_KEY_ID = 0x02, /* use TMP_KEY_ID column, by default not opened */
ewalgn_co_PLOIDY = 0x04, /* ploidy is more than 1, columns PLOIDY, READ_START, READ_LEN needs data */
ewalgn_co_unsorted = 0x08, /* use the unsorted table scheme */
ewalgn_co_MATE_ALIGN_ID_only = 0x10, /* disable all other MATE_* columns */
ewalgn_co_MISMATCH_QUALITY = 0x20, /* enable MISMATCH_QUALITY column */
ewalgn_co_MATE_POSITION = 0x40 /* enable mate position columns */
};
typedef struct TableWriterAlgnData_struct {
TableWriterData seq_spot_id;
TableWriterData seq_read_id;
TableWriterData tmp_key_id;
/* BEGIN filled out by ReferenceMgr_Compress */
uint32_t ploidy; /* incremented sequentially for each call, must be set to 0 for each new spot */
TableWriterData read_start; /* mandatory */
TableWriterData read_len; /* mandatory */
TableWriterData has_ref_offset; /* mandatory */
TableWriterData ref_offset; /* mandatory */
TableWriterData ref_offset_type; /* mandatory */
TableWriterData ref_id; /* used for unsorted*/
TableWriterData ref_start; /* used only for unsorted */
TableWriterData global_ref_start; /* used only for sorted */
TableWriterData has_mismatch; /* mandatory only for primary */
TableWriterData mismatch; /* mandatory only for primary */
TableWriterData mismatch_qual;
INSDC_coord_len ref_len; /* projection on refseq is same for all alleles! */
/* tmp data, never saved to db */
/* recalculated offset in reference based on CIGAR and circularity in Compression */
INSDC_coord_zero effective_offset;
int64_t ref_1st_row_id;
/* END filled out by ReferenceMgr_Compress */
TableWriterData ref_orientation;
TableWriterData ref_ploidy;
TableWriterData mapq;
TableWriterData align_group; /* set length to 0 if not used */
TableWriterData linkageGroup; /* set length to 0 if not used */
/* used only only in secondary */
TableWriterData mate_ref_orientation;
TableWriterData mate_ref_id;
TableWriterData mate_ref_pos;
TableWriterData mate_align_id;
TableWriterData template_len;
/* used only in for ewalgn_tabletype_EvidenceInterval table type */
TableWriterData alingment_ids;
} TableWriterAlgnData;
typedef struct TableWriterAlgn TableWriterAlgn;
typedef union ReferenceStart ReferenceStart;
union ReferenceStart {
uint64_t global_ref_start;
struct {
int64_t ref_id;
INSDC_coord_one ref_start;
} local;
};
ALIGN_EXTERN rc_t CC TableWriterAlgn_Make(const TableWriterAlgn** cself, VDatabase* db,
ETableWriterAlgn_TableType type, uint32_t options);
/* rows optional here */
ALIGN_EXTERN rc_t CC TableWriterAlgn_Whack(const TableWriterAlgn* cself, bool commit, uint64_t* rows);
ALIGN_EXTERN rc_t CC TableWriterAlgn_WriteDefault(const TableWriterAlgn* cself,
enum ETableWriterAlgn_ColNames col, const TableWriterData* data);
ALIGN_EXTERN rc_t CC TableWriterAlgn_GetNextRowId(const TableWriterAlgn* cself, int64_t* rowid);
/* rowid optional here */
ALIGN_EXTERN rc_t CC TableWriterAlgn_Write(const TableWriterAlgn* cself, const TableWriterAlgnData* data, int64_t* rowid);
/* closes main cursor and creates lookup object on the successfully committed main cursor */
ALIGN_EXTERN rc_t CC TableWriterAlgn_TmpKeyStart(const TableWriterAlgn* cself);
/* retrieve TMP_KEY value by rowid */
ALIGN_EXTERN rc_t CC TableWriterAlgn_TmpKey(const TableWriterAlgn* cself, int64_t rowid, uint64_t* key_id);
/* retrieve reference start value by rowid */
ALIGN_EXTERN rc_t CC TableWriterAlgn_RefStart(const TableWriterAlgn* cself, int64_t rowid, ReferenceStart *const rslt);
/* assign a SPOT_ID value to row */
ALIGN_EXTERN rc_t CC TableWriterAlgn_Write_SpotId(const TableWriterAlgn* cself, int64_t rowid, int64_t spot_id);
ALIGN_EXTERN rc_t CC TableWriterAlgn_Write_SpotInfo(const TableWriterAlgn* cself,
int64_t rowid,
int64_t spot_id,
int64_t mate_id,
ReferenceStart const *ref_start);
#ifdef __cplusplus
}
#endif
#endif /* _h_align_writer_alignment_ */
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