/usr/include/ngs/itf/ReadCollectionItf.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_read_collectionitf_
#define _h_ngs_itf_read_collectionitf_
#ifndef _h_ngs_itf_vtable_
#include "VTable.h"
#endif
#ifdef __cplusplus
extern "C" {
#endif
/*--------------------------------------------------------------------------
* forwards
*/
struct NGS_Read_v1;
struct NGS_ReadGroup_v1;
struct NGS_Reference_v1;
struct NGS_Alignment_v1;
/*--------------------------------------------------------------------------
* NGS_ReadCollection_v1
*/
typedef struct NGS_ReadCollection_v1 NGS_ReadCollection_v1;
struct NGS_ReadCollection_v1
{
const NGS_VTable * vt;
};
typedef struct NGS_ReadCollection_v1_vt NGS_ReadCollection_v1_vt;
struct NGS_ReadCollection_v1_vt
{
NGS_VTable dad;
// 1.0
NGS_String_v1 * ( CC * get_name ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err );
struct NGS_ReadGroup_v1 * ( CC * get_read_groups ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err );
struct NGS_ReadGroup_v1 * ( CC * get_read_group ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, const char * spec );
struct NGS_Reference_v1 * ( CC * get_references ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err );
struct NGS_Reference_v1 * ( CC * get_reference ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, const char * spec );
struct NGS_Alignment_v1 * ( CC * get_alignment ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
const char * alignmentId );
struct NGS_Alignment_v1 * ( CC * get_alignments ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_primary, bool wants_secondary );
uint64_t ( CC * get_align_count ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_primary, bool wants_secondary );
struct NGS_Alignment_v1 * ( CC * get_align_range ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t first, uint64_t count, bool wants_primary, bool wants_secondary );
struct NGS_Read_v1 * ( CC * get_read ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, const char * readId );
struct NGS_Read_v1 * ( CC * get_reads ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned );
uint64_t ( CC * get_read_count ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err, bool wants_full, bool wants_partial, bool wants_unaligned );
struct NGS_Read_v1 * ( CC * get_read_range ) ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
// 1.1
bool ( CC * has_read_group ) ( const NGS_ReadCollection_v1 * self, const char * spec );
bool ( CC * has_reference ) ( const NGS_ReadCollection_v1 * self, const char * spec );
};
#ifdef __cplusplus
}
#endif
#endif /* _h_ngs_itf_read_collectionitf_ */
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