/usr/include/ncbi-vdb/loader/common-writer.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_common_writer_
#define _h_common_writer_
#ifndef _h_klib_defs_
#include <klib/defs.h>
#endif
#ifndef _h_insdc_sra_
#include <insdc/sra.h>
#endif
#ifndef _h_mmarray_
#include <loader/mmarray.h>
#endif
#ifdef __cplusplus
extern "C" {
#endif
/*--------------------------------------------------------------------------
* forwards
*/
struct VDBManager;
struct VDatabase;
struct KMemBank;
struct KBTree;
struct KLoadProgressbar;
struct ReaderFile;
struct CommonWriter;
struct SequenceWriter;
struct AlignmentWriter;
struct Reference;
/*--------------------------------------------------------------------------
* CommonWriterSettings
*/
enum LoaderModes {
mode_Archive,
mode_Analysis
};
typedef struct CommonWriterSettings
{
uint64_t numfiles;
char const *inpath;
char const *outpath;
char const *tmpfs;
struct KFile *noMatchLog;
char const *schemaPath;
char const *schemaIncludePath;
char const *refXRefPath;
char const *QualQuantizer;
char const *refFilter;
char const** refFiles; /* NULL-terminated array pointing to argv */
char const *headerText;
uint64_t maxAlignCount;
size_t cache_size;
uint64_t errCount;
uint64_t maxErrCount;
uint64_t maxErrPct;
uint64_t maxWarnCount_NoMatch;
uint64_t maxWarnCount_DupConflict;
uint64_t pid;
uint64_t minMatchCount; /* minimum number of matches to count as an alignment */
int minMapQual;
enum LoaderModes mode;
uint32_t maxSeqLen;
bool omit_aligned_reads;
bool omit_reference_reads;
bool no_real_output;
bool expectUnsorted;
bool noVerifyReferences;
bool onlyVerifyReferences;
bool useQUAL;
bool limit2config;
bool editAlignedQual;
bool keepMismatchQual;
bool acceptBadDups; /* accept spots with inconsistent PCR duplicate flags */
bool acceptNoMatch; /* accept without any matching bases */
uint8_t alignedQualValue;
bool allUnaligned; /* treat all records as unaligned */
bool noColorSpace;
bool noSecondary;
bool hasTI;
bool acceptHardClip;
INSDC_SRA_platform_id platform;
bool parseSpotName;
bool compressQuality;
uint64_t maxMateDistance;
} CommonWriterSettings;
/*--------------------------------------------------------------------------
* SpotAssembler
*/
#define FRAG_CHUNK_SIZE (128)
typedef struct SpotAssembler {
const struct KLoadProgressbar *progress[4];
struct KBTree *key2id[NUM_ID_SPACES];
char *key2id_names;
struct MMArray *id2value;
struct KMemBank *fragsBoth; /*** mate will be there soon ***/
struct KMemBank *fragsOne; /*** mate may not be found soon or even show up ***/
int64_t spotId;
int64_t primaryId;
int64_t secondId;
uint64_t alignCount;
uint32_t idCount[NUM_ID_SPACES];
uint32_t key2id_hash[NUM_ID_SPACES];
size_t key2id_max;
size_t key2id_name_max;
size_t key2id_name_alloc;
size_t key2id_count;
size_t key2id_name[NUM_ID_SPACES];
/* this array is kept in name order */
/* this maps the names to key2id and idCount */
size_t key2id_oid[NUM_ID_SPACES];
unsigned pass;
bool isColorSpace;
} SpotAssembler;
INSDC_SRA_platform_id PlatformToId(const char* name);
/*--------------------------------------------------------------------------
* CommonWriter
*/
typedef struct CommonWriter {
CommonWriterSettings settings;
SpotAssembler ctx;
struct Reference* ref;
struct SequenceWriter* seq;
struct AlignmentWriter* align;
bool had_alignments;
bool had_sequences;
unsigned err_count;
bool commit;
} CommonWriter;
rc_t CommonWriterInit(CommonWriter* self, struct VDBManager *mgr, struct VDatabase *db, const CommonWriterSettings* settings);
rc_t CommonWriterArchive(CommonWriter* self, const struct ReaderFile *);
rc_t CommonWriterComplete(CommonWriter* self, bool quitting, uint64_t maxDistance);
rc_t CommonWriterWhack(CommonWriter* self);
#ifdef __cplusplus
}
#endif
#endif /* _h_common_writer_ */
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