/usr/include/ncbi-vdb/loader/common-reader-priv.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 | /*===========================================================================
*
* 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_reader_priv_
#define _h_common_reader_priv_
#include <loader/common-reader.h>
#include <klib/refcount.h>
#include <klib/text.h>
#include <klib/data-buffer.h>
#ifdef __cplusplus
extern "C" {
#endif
/*TODO: add module rcLoader to rc.h? */
#define RC_MODULE rcAlign
/*--------------------------------------------------------------------------
ReaderFile
*/
#ifndef READERFILE_IMPL
#define READERFILE_IMPL struct ReaderFile
#endif
typedef struct ReaderFile_vt_v1_struct {
/* version == 1.x */
uint32_t maj;
uint32_t min;
/* start minor version == 0 */
rc_t ( *destroy ) ( READERFILE_IMPL* self );
rc_t ( *getRecord ) ( const READERFILE_IMPL *self, const Record** result );
float ( *getProportionalPosition ) ( const READERFILE_IMPL *self );
rc_t ( *getReferenceInfo ) ( const READERFILE_IMPL *self, const ReferenceInfo** result );
/* end minor version == 0 */
} ReaderFile_vt_v1;
typedef union ReaderFile_vt {
ReaderFile_vt_v1* v1;
} ReaderFile_vt;
struct ReaderFile
{
ReaderFile_vt vt;
KRefcount refcount;
char* pathname;
};
/* Init
* polymorphic parent constructor
*/
rc_t CC ReaderFileInit ( READERFILE_IMPL *self );
/* Whack
* destructor
*/
rc_t CC ReaderFileWhack ( ReaderFile *self );
/*--------------------------------------------------------------------------
Record
*/
#ifndef RECORD_IMPL
#define RECORD_IMPL struct Record
#endif
typedef struct Record_vt_v1_struct {
/* version == 1.x */
uint32_t maj;
uint32_t min;
/* start minor version == 0 */
rc_t ( *addRef ) ( const RECORD_IMPL* self );
rc_t ( *release ) ( const RECORD_IMPL* self );
rc_t ( *getSequence ) ( const RECORD_IMPL *self, const Sequence** result );
rc_t ( *getAlignment ) ( const RECORD_IMPL *self, const Alignment** result );
rc_t ( *getRejected ) ( const RECORD_IMPL *self, const Rejected** result );
/* end minor version == 0 */
} Record_vt_v1;
typedef union Record_vt {
Record_vt_v1* v1;
} Record_vt;
struct Record
{
Record_vt vt;
};
/*--------------------------------------------------------------------------
Sequence
*/
#ifndef SEQUENCE_IMPL
#define SEQUENCE_IMPL struct Sequence
#endif
typedef struct Sequence_vt_v1_struct {
/* version == 1.x */
uint32_t maj;
uint32_t min;
/* start minor version == 0 */
rc_t ( *addRef ) ( const SEQUENCE_IMPL* self );
rc_t ( *release ) ( const SEQUENCE_IMPL* self );
rc_t ( *getReadLength ) ( const SEQUENCE_IMPL *self, uint32_t *length );
rc_t ( *getRead ) ( const SEQUENCE_IMPL *self, char *sequence );
rc_t ( *getRead2 ) ( const SEQUENCE_IMPL *self, char *sequence, uint32_t start, uint32_t stop );
rc_t ( *getQuality ) ( const SEQUENCE_IMPL *self, const int8_t **quality, uint8_t *offset, int *qualType );
rc_t ( *getSpotGroup ) ( const SEQUENCE_IMPL *self, const char **name, size_t *length );
rc_t ( *getSpotName ) ( const SEQUENCE_IMPL *self, const char **name, size_t *length );
bool ( *isColorSpace ) ( const SEQUENCE_IMPL *self );
rc_t ( *getCSKey ) ( const SEQUENCE_IMPL *self, char cskey[1] );
rc_t ( *getCSReadLength ) ( const SEQUENCE_IMPL *self, uint32_t *length );
rc_t ( *getCSRead ) ( const SEQUENCE_IMPL *self, char *sequence );
rc_t ( *getCSQuality ) ( const SEQUENCE_IMPL *self, const int8_t **quality, uint8_t *offset, int *qualType );
bool ( *wasPaired ) ( const SEQUENCE_IMPL *self );
int ( *orientationSelf ) ( const SEQUENCE_IMPL *self );
int ( *orientationMate ) ( const SEQUENCE_IMPL *self );
bool ( *isFirst ) ( const SEQUENCE_IMPL *self );
bool ( *isSecond ) ( const SEQUENCE_IMPL *self );
bool ( *isDuplicate ) ( const SEQUENCE_IMPL *self );
bool ( *isLowQuality ) ( const SEQUENCE_IMPL *self );
rc_t ( *getTI ) ( const SEQUENCE_IMPL *self, uint64_t *ti );
/* end minor version == 0 */
} Sequence_vt_v1;
typedef union Sequence_vt {
Sequence_vt_v1* v1;
} Sequence_vt;
struct Sequence
{
Sequence_vt vt;
};
/*--------------------------------------------------------------------------
Alignment
*/
#ifndef ALIGNMENT_IMPL
#define ALIGNMENT_IMPL struct Alignment
#endif
typedef struct Alignment_vt_v1_struct {
/* version == 1.x */
uint32_t maj;
uint32_t min;
/* start minor version == 0 */
rc_t ( *addRef ) ( const ALIGNMENT_IMPL* self );
rc_t ( *release ) ( const ALIGNMENT_IMPL* self );
rc_t ( *getRefSeqId ) ( const ALIGNMENT_IMPL *self, int32_t *refSeqId );
rc_t ( *getMateRefSeqId ) ( const ALIGNMENT_IMPL *self, int32_t *refSeqId );
rc_t ( *getPosition ) ( const ALIGNMENT_IMPL *self, int64_t *pos );
rc_t ( *getMatePosition ) ( const ALIGNMENT_IMPL *self, int64_t *pos );
rc_t ( *getMapQuality ) ( const ALIGNMENT_IMPL *self, uint8_t *qual );
rc_t ( *getAlignmentDetail ) ( const ALIGNMENT_IMPL *self, AlignmentDetail *rslt, uint32_t count, uint32_t *actual, int32_t *firstMatch, int32_t *lastMatch );
rc_t ( *getAlignOpCount ) ( const ALIGNMENT_IMPL *self, uint32_t *n );
rc_t ( *getInsertSize ) ( const ALIGNMENT_IMPL *self, int64_t *size );
rc_t ( *getCG ) ( const ALIGNMENT_IMPL *self, const CGData** result );
rc_t ( *getBAMCigar ) ( const ALIGNMENT_IMPL *self, uint32_t const **rslt, uint32_t *length );
bool ( *isSecondary ) ( const ALIGNMENT_IMPL *self );
/* end minor version == 0 */
} Alignment_vt_v1;
typedef union Alignment_vt {
Alignment_vt_v1* v1;
} Alignment_vt;
struct Alignment
{
Alignment_vt vt;
};
/*--------------------------------------------------------------------------
CGData
*/
#ifndef CGDATA_IMPL
#define CGDATA_IMPL struct CGData
#endif
typedef struct CGData_vt_v1_struct {
/* version == 1.x */
uint32_t maj;
uint32_t min;
/* start minor version == 0 */
rc_t ( *addRef ) ( const CGDATA_IMPL* self );
rc_t ( *release ) ( const CGDATA_IMPL* self );
rc_t ( * getSeqQual ) ( const CGDATA_IMPL* self, char sequence[/* 35 */], uint8_t quality[/* 35 */] );
rc_t ( * getCigar ) ( const CGDATA_IMPL* self, uint32_t *cigar, uint32_t cig_max, uint32_t *cig_act );
rc_t ( * getAlignGroup ) ( const CGDATA_IMPL* self, char buffer[], size_t max_size, size_t *act_size);
/* end minor version == 0 */
} CGData_vt_v1;
typedef union CGData_vt {
CGData_vt_v1* v1;
} CGData_vt;
struct CGData
{
CGData_vt vt;
};
/*--------------------------------------------------------------------------
Rejected
*/
struct Rejected {
KRefcount refcount;
String source;
const char* message;
uint64_t line;
uint64_t column;
bool fatal;
};
rc_t CC RejectedInit ( Rejected *self );
/*--------------------------------------------------------------------------
ReferenceInfo
*/
#ifndef REFERENCEINFO_IMPL
#define REFERENCEINFO_IMPL struct ReferenceInfo
#endif
typedef struct ReferenceInfo_vt_v1_struct {
/* version == 1.x */
uint32_t maj;
uint32_t min;
/* start minor version == 0 */
rc_t ( *addRef ) ( const REFERENCEINFO_IMPL* self );
rc_t ( *release ) ( const REFERENCEINFO_IMPL* self );
rc_t ( *getRefSeqCount ) ( const REFERENCEINFO_IMPL* self, uint32_t* count );
rc_t ( *getRefSeq ) ( const REFERENCEINFO_IMPL* self, uint32_t n, ReferenceSequence* result );
rc_t ( *getReadGroupCount ) ( const REFERENCEINFO_IMPL* self, uint32_t* count );
rc_t ( *getReadGroup ) ( const REFERENCEINFO_IMPL* self, unsigned n, ReadGroup* result );
rc_t ( *getReadGroupByName ) ( const REFERENCEINFO_IMPL* self, const char* name, ReadGroup* result );
/* end minor version == 0 */
} ReferenceInfo_vt_v1;
typedef union ReferenceInfo_vt {
ReferenceInfo_vt_v1* v1;
} ReferenceInfo_vt;
struct ReferenceInfo
{
ReferenceInfo_vt vt;
};
#ifdef __cplusplus
}
#endif
#endif /* _h_common_reader_priv_ */
|