/usr/include/ngs/itf/AlignmentItf.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.
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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_ngs_itf_alignmentitf_
#define _h_ngs_itf_alignmentitf_
#ifndef _h_ngs_itf_vtable_
#include <ngs/itf/VTable.h>
#endif
#ifdef __cplusplus
extern "C" {
#endif
/*--------------------------------------------------------------------------
* NGS_Alignment_v1
*/
typedef struct NGS_Alignment_v1 NGS_Alignment_v1;
struct NGS_Alignment_v1
{
const NGS_VTable * vt;
};
typedef struct NGS_Alignment_v1_vt NGS_Alignment_v1_vt;
struct NGS_Alignment_v1_vt
{
NGS_VTable dad;
/* v1.0 interface */
NGS_String_v1 * ( CC * get_id ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_ref_spec ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
int32_t ( CC * get_map_qual ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_ref_bases ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_read_group ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_read_id ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_clipped_frag_bases ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_clipped_frag_quals ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_aligned_frag_bases ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
bool ( CC * is_primary ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
int64_t ( CC * get_align_pos ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
uint64_t ( CC * get_align_length ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
bool ( CC * get_is_reversed ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
int32_t ( CC * get_soft_clip ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err, uint32_t edge );
uint64_t ( CC * get_template_len ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_short_cigar ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err, bool clipped );
NGS_String_v1 * ( CC * get_long_cigar ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err, bool clipped );
bool ( CC * has_mate ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_mate_id ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_Alignment_v1 * ( CC * get_mate_alignment ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
NGS_String_v1 * ( CC * get_mate_ref_spec ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
bool ( CC * get_mate_is_reversed ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
bool ( CC * next ) ( NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
/* v1.1 */
char ( CC * get_rna_orientation ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err );
/* v1.2 */
uint64_t ( CC * get_ref_pos_projection_range ) ( const NGS_Alignment_v1 * self, NGS_ErrBlock_v1 * err, int64_t ref_pos );
};
#ifdef __cplusplus
}
#endif
#endif /* _h_ngs_itf_alignmentitf_ */
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