/usr/include/ncbi-vdb/fastq/fq-dump.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 | /*===========================================================================
*
* 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_fastq_fq_dump_
#define _h_fastq_fq_dump_
#ifndef _h_fastq_extern_
#include <fastq/extern.h>
#endif
#ifdef __cplusplus
extern "C" {
#endif
/*--------------------------------------------------------------------------
* FastqDumper
* an object capable of producing fastq
*/
typedef struct FastqDumper FastqDumper;
/* AddRef
* Release
* all objects are reference counted
* NULL references are ignored
*/
FASTQ_EXTERN rc_t CC FastqDumperAddRef ( const FastqDumper *self );
FASTQ_EXTERN rc_t CC FastqDumperRelease ( const FastqDumper *self );
/* FastqDumperMake
* make an empty dumper
*/
FASTQ_EXTERN rc_t CC FastqDumperMake ( FastqDumper **fastq );
/* FastqDumperAddSource
* adds an accession/filename/url to be processed
*/
FASTQ_EXTERN rc_t CC FastqDumperAddSource ( FastqDumper *self, const char * name );
/* FastqDumperEnableSpotSplitting
* spot-splitting is OFF per default
*/
FASTQ_EXTERN rc_t CC FastqDumperEnableSpotSplit ( FastqDumper *self );
/* FastqDumperEnableClipping
* clipping is OFF per default
*/
FASTQ_EXTERN rc_t CC FastqDumperEnableClipping ( FastqDumper *self );
/* FastqDumperAddRowRange
* default is processing all rows in the source(s)
*/
FASTQ_EXTERN rc_t CC FastqDumperAddRowRange ( FastqDumper *self, int64_t range_start, uint64_t count );
/* FastqDumperEstimate
* estimates ( because of filtering ) the number of fastq-records
* for gui-tools to setup a progress-bar
*/
FASTQ_EXTERN rc_t CC FastqDumperEstimate ( const FastqDumper *self, uint64_t * count );
/* FastqDumperSetCallback
* the function will be called for every "fastq-record"
*/
FASTQ_EXTERN rc_t CC FastqDumperSetCallback ( FastqDumper *self,
void *data, void ( CC * on_record ) ( uint64_t nr, uint32_t length,
const char * seq_id, const char *name,
const char * read, const char * quality ) );
/* FastqDumperPerform
* performs the requested operations
*/
FASTQ_EXTERN rc_t CC FastqDumperPerform ( const FastqDumper *self );
#ifdef __cplusplus
}
#endif
#endif /* _h_fastq_fq_dump_ */
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