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_read_
28 #define _h_csra1_read_
29 
30 typedef struct CSRA1_Read CSRA1_Read;
31 
32 #ifndef NGS_READ
33 #define NGS_READ CSRA1_Read
34 #endif
35 
36 #ifndef _h_sra_read_
37 #include "SRA_Read.h"
38 #endif
39 
40 
41 #ifdef __cplusplus
42 extern "C" {
43 #endif
44 
45 /*--------------------------------------------------------------------------
46  * forwards
47  */
48 
49 /*--------------------------------------------------------------------------
50  * CSRA1_Read
51  */
52 
53 /* Make
54  * a single read
55  */
56 struct NGS_Read * CSRA1_ReadMake ( ctx_t ctx, const struct NGS_Cursor * curs, int64_t readId, const struct NGS_String * spec );
57 
58 /* IteratorMake
59  */
60 struct NGS_Read * CSRA1_ReadIteratorMake ( ctx_t ctx,
61                                                const struct NGS_Cursor * curs,
62                                                const struct NGS_String * run_name,
63                                                bool wants_full,
64                                                bool wants_partial,
65                                                bool wants_unaligned );
66 
67 /* IteratorMakeRange
68  * all reads in the specified range of rowIds
69  */
70 struct NGS_Read * CSRA1_ReadIteratorMakeRange ( ctx_t ctx,
71                                               const struct NGS_Cursor * curs,
72                                               const struct NGS_String * run_name,
73                                               uint64_t first,
74                                               uint64_t count,
75                                               bool wants_full,
76                                               bool wants_partial,
77                                               bool wants_unaligned );
78 
79 /* IteratorMakeReadGroup
80  * within the specified range of rowIds, will only return reads belonging to the specified read group (groupName)
81  */
82 struct NGS_Read * CSRA1_ReadIteratorMakeReadGroup ( ctx_t ctx,
83                                                   const struct NGS_Cursor * curs,
84                                                   const struct NGS_String * run_name,
85                                                   const struct NGS_String * group_name,
86                                                   uint64_t first,
87                                                   uint64_t count,
88                                                   bool wants_full,
89                                                   bool wants_partial,
90                                                   bool wants_unaligned );
91 
92 #ifdef __cplusplus
93 }
94 #endif
95 
96 #endif /* _h_csra1_read_ */
97