/usr/include/ngs/itf/ReferenceItf.h is in libngs-sdk-dev 1.3.0-2.
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 | /*===========================================================================
*
* 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_ngs_itf_referenceitf_
#define _h_ngs_itf_referenceitf_
#ifndef _h_ngs_itf_vtable_
#include "VTable.h"
#endif
#ifdef __cplusplus
extern "C" {
#endif
/*--------------------------------------------------------------------------
* forwards
*/
struct NGS_Pileup_v1;
struct NGS_Alignment_v1;
enum NGS_ReferenceAlignFlags
{
NGS_ReferenceAlignFlags_wants_primary = 0x01,
NGS_ReferenceAlignFlags_wants_secondary = 0x02,
NGS_ReferenceAlignFlags_pass_bad = 0x04,
NGS_ReferenceAlignFlags_pass_dups = 0x08,
NGS_ReferenceAlignFlags_min_map_qual = 0x10,
NGS_ReferenceAlignFlags_max_map_qual = 0x20,
NGS_ReferenceAlignFlags_no_wraparound = 0x40,
NGS_ReferenceAlignFlags_start_within_window = 0x80
};
/*--------------------------------------------------------------------------
* NGS_Reference_v1
*/
typedef struct NGS_Reference_v1 NGS_Reference_v1;
struct NGS_Reference_v1
{
const NGS_VTable * vt;
};
typedef struct NGS_Reference_v1_vt NGS_Reference_v1_vt;
struct NGS_Reference_v1_vt
{
NGS_VTable dad;
/* v1.0 interface */
NGS_String_v1 * ( CC * get_cmn_name ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_canon_name ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
bool ( CC * is_circular ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
uint64_t ( CC * get_length ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_ref_bases ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, uint64_t offset, uint64_t length );
NGS_String_v1 * ( CC * get_ref_chunk ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, uint64_t offset, uint64_t length );
struct NGS_Alignment_v1 * ( CC * get_alignment ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, const char * alignmentId );
struct NGS_Alignment_v1 * ( CC * get_alignments ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, bool wants_primary, bool wants_secondary );
struct NGS_Alignment_v1 * ( CC * get_align_slice ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
int64_t start, uint64_t length, bool wants_primary, bool wants_secondary );
struct NGS_Pileup_v1 * ( CC * get_pileups ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, bool wants_primary, bool wants_secondary );
struct NGS_Pileup_v1 * ( CC * get_pileup_slice ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err,
int64_t start, uint64_t length, bool wants_primary, bool wants_secondary );
bool ( CC * next ) ( NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err );
/* v1.1 interface */
struct NGS_Pileup_v1 * ( CC * get_filtered_pileups ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, uint32_t flags, int32_t map_qual );
struct NGS_Pileup_v1 * ( CC * get_filtered_pileup_slice ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, int64_t start, uint64_t length, uint32_t flags, int32_t map_qual );
/* 1.2 interface */
uint64_t ( CC * get_align_count ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, bool wants_primary, bool wants_secondary );
/* 1.3 interface */
struct NGS_Alignment_v1 * ( CC * get_filtered_alignments ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, uint32_t flags, int32_t map_qual );
struct NGS_Alignment_v1 * ( CC * get_filtered_align_slice ) ( const NGS_Reference_v1 * self, NGS_ErrBlock_v1 * err, int64_t start, uint64_t length, uint32_t flags, int32_t map_qual );
};
#ifdef __cplusplus
}
#endif
#endif /* _h_ngs_itf_referenceitf_ */
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