This file is indexed.

/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.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
/*===========================================================================
 *
 *                            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_ */