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comparison libs/sratoolkit.2.8.0-centos_linux64/schema/align/mate-cache.vschema @ 3:38ad1130d077 draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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2:0d65b71ff8df 3:38ad1130d077
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 /*==========================================================================
28 * VDB mate-cache types, functions and tables
29 */
30 version 1;
31
32 include 'insdc/insdc.vschema';
33 include 'vdb/vdb.vschema';
34 include 'insdc/sra.vschema';
35
36
37 /*--------------------------------------------------------------------------
38 * data types
39 */
40
41
42 /*--------------------------------------------------------------------------
43 * functions
44 */
45
46
47 /*--------------------------------------------------------------------------
48 * tables
49 */
50
51 table NCBI:align:tbl:mate_cache #1.1
52 {
53 /* SAM_FLAGS
54 */
55 extern column < U32 > izip_encoding SAM_FLAGS_CACHE;
56
57 /* SAM_QUALITY
58 */
59 extern column < INSDC:quality:text:phred_33 > zip_encoding SAM_QUALITY_CACHE;
60
61 /* TEMPLATE_LEN
62 */
63 extern column < I32 > izip_encoding TEMPLATE_LEN_CACHE;
64
65 /* MATE_ALIGN_ID
66 */
67 extern column < I64 > izip_encoding MATE_ALIGN_ID_CACHE;
68
69 /* MATE_REF_NAME
70 */
71 extern column < ascii > zip_encoding MATE_REF_NAME_CACHE;
72
73 /* MATE_REF_POS
74 */
75 extern column < INSDC:coord:zero > izip_encoding MATE_REF_POS_CACHE;
76
77 /* ALIGNMENT_COUNT
78 */
79 extern column < U8 > izip_encoding ALIGNMENT_COUNT_CACHE;
80
81 /* RD_FILTER
82 */
83 extern column < INSDC:SRA:read_filter > zip_encoding RD_FILTER_CACHE;
84 readonly column INSDC:SRA:read_filter READ_FILTER_CACHE = .RD_FILTER_CACHE;
85
86 /* SPOT_GROUP
87 */
88 extern column < ascii > zip_encoding SPOT_GROUP_CACHE;
89 readonly column ascii SEQ_SPOT_GROUP_CACHE = .SPOT_GROUP_CACHE;
90 };
91
92 /*--------------------------------------------------------------------------
93 * databases
94 */
95
96 database NCBI:align:db:mate_cache #1
97 {
98 table NCBI:align:tbl:mate_cache #1.1 PRIMARY_ALIGNMENT;
99 };