1 /*===========================================================================
2 *
3 *                            PUBLIC DOMAIN NOTICE
4 *               National Center for Biotechnology Information
5 *
6 *  This software/database is a "United States Government Work" under the
7 *  terms of the United States Copyright Act.  It was written as part of
8 *  the author's official duties as a United States Government employee and
9 *  thus cannot be copyrighted.  This software/database is freely available
10 *  to the public for use. The National Library of Medicine and the U.S.
11 *  Government have not placed any restriction on its use or reproduction.
12 *
13 *  Although all reasonable efforts have been taken to ensure the accuracy
14 *  and reliability of the software and data, the NLM and the U.S.
15 *  Government do not and cannot warrant the performance or results that
16 *  may be obtained by using this software or data. The NLM and the U.S.
17 *  Government disclaim all warranties, express or implied, including
18 *  warranties of performance, merchantability or fitness for any particular
19 *  purpose.
20 *
21 *  Please cite the author in any work or product based on this material.
22 *
23 * ===========================================================================
24 *
25 */
26 
27 #ifndef _h_csra1_reference_window_
28 #define _h_csra1_reference_window_
29 
30 #ifndef _h_kfc_defs_
31 #include <kfc/defs.h>
32 #endif
33 
34 #ifdef __cplusplus
35 extern "C" {
36 #endif
37 
38 /*--------------------------------------------------------------------------
39  * forwards
40  */
41 
42 struct NGS_Cursor;
43 struct NGS_Alignment;
44 struct NGS_ReadCollection;
45 
46 struct NGS_Alignment * CSRA1_ReferenceWindowMake ( ctx_t ctx,
47                                                    struct NGS_ReadCollection * coll,
48                                                    const struct NGS_Cursor* curs,
49                                                    bool circular,
50                                                    uint64_t ref_length,
51                                                    uint32_t chunk_size,
52                                                    int64_t primary_begin_row,
53                                                    int64_t secondary_begin_row,
54                                                    int64_t end_row,
55                                                    uint64_t offset,
56                                                    uint64_t size, /* 0 - all remaining */
57                                                    bool wants_primary,
58                                                    bool wants_secondary,
59                                                    uint32_t filters,
60                                                    int32_t map_qual,
61                                                    uint64_t id_offset );
62 
63 #ifdef __cplusplus
64 }
65 #endif
66 
67 #endif /* _h_csra1_alignment_ */
68