/usr/lib/ncbi-vdb/ncbi/seq-graph.vschema is in libncbi-vdb2 2.8.2-2+dfsg-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 | /*===========================================================================
*
* 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.
*
* ===========================================================================
*
*/
/*==========================================================================
* seq-graph style named annotations
*/
version 1;
include '/usr/lib/ncbi-vdb/vdb/vdb.vschema';
/*--------------------------------------------------------------------------
* types
* constants
*/
// example usage of data type:
typedef utf8 NCBI:SeqGraph:sid;
typedef utf8 NCBI:SeqGraph:name;
typedef U32 NCBI:SeqGraph:len;
typedef U32 NCBI:SeqGraph:scale;
typedef I64 NCBI:SeqGraph:value;
typedef NCBI:SeqGraph:value NCBI:SeqGraph:start;
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q0; // min
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q10; // 10th quantile
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q50; // median
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q90; // 90th quantile
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q100; // max
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q0; // min zoomed to 100bp segment
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q10; // 10th quantile zoomed to 100bp segment
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q50; // median zoomed to 100bp segment
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q90; // 90th quantile zoomed to 100bp segment
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q100; // max zoomed to 100bp segment
typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_num_switches; // number of value switches in graph
/*--------------------------------------------------------------------------
* tables
*/
table NCBI:SeqGraph:tbl:seqgraph #1.0
{
/* SID
* Sequence id (Accession.version).
* Indexed.
*/
extern column NCBI:SeqGraph:sid SID
= ( NCBI:SeqGraph:sid ) idx:text:project #1.0 < 'sid' > ( .SID );
physical column < NCBI:SeqGraph:sid > zip_encoding .SID
= ( NCBI:SeqGraph:sid ) idx:text:insert #1.0 < 'sid' > ( SID );
/* NAME
* Sequence name (which resolves into SID using assembly information)
* Indexed.
*/
extern column NCBI:SeqGraph:name NAME
= ( NCBI:SeqGraph:name ) idx:text:project #1.0 < 'name' > ( .NAME );
physical column < NCBI:SeqGraph:name > zip_encoding .NAME
= ( NCBI:SeqGraph:name ) idx:text:insert #1.0 < 'name' > ( NAME );
/* START
* Sequence offset for the segment saved in this row.
* In most cases this can be calculated from row id and LEN below.
*/
extern column < NCBI:SeqGraph:start > izip_encoding START;
/* LEN
* MAX_SEQ_LEN is used in our refseq schema
* CHUNK_SIZE might be preferred
* Mostly a constant ( = 5000), except for the last row for each sequence.
*/
extern column < NCBI:SeqGraph:len > izip_encoding LEN;
/* SCALE
* Scaling factor for graph values.
* Mostly needed in order to store values as integers when actual values
* are real with a certain precision.
*/
extern column < NCBI:SeqGraph:scale > izip_encoding SCALE;
/* GRAPH
* intensity values
*/
extern column < NCBI:SeqGraph:value > izip_encoding GRAPH;
/* GR_Q0
* Minimal value for the row
*/
extern column < NCBI:SeqGraph:gr_q0 > izip_encoding GR_Q0;
/* GR_Q10
* 10th quantile value for the row
*/
extern column < NCBI:SeqGraph:gr_q10 > izip_encoding GR_Q10;
/* GR_Q50
* Median value for the row
*/
extern column < NCBI:SeqGraph:gr_q50 > izip_encoding GR_Q50;
/* GR_Q90
* 90th quantile value for the row
*/
extern column < NCBI:SeqGraph:gr_q90 > izip_encoding GR_Q90;
/* GR_Q100
* Maximal value for the row
*/
extern column < NCBI:SeqGraph:gr_q100 > izip_encoding GR_Q100;
/* GR_ZOOM_Q0
* Minimal values for 100bp segments of the graph chunk
*/
extern column < NCBI:SeqGraph:gr_zoom_q0 > izip_encoding GR_ZOOM_Q0;
/* GR_ZOOM_Q10
* 10th quantile values for 100bp segments of the graph chunk
*/
extern column < NCBI:SeqGraph:gr_zoom_q10 > izip_encoding GR_ZOOM_Q10;
/* GR_ZOOM_Q50
* Median values for 100bp segments of the graph chunk
*/
extern column < NCBI:SeqGraph:gr_zoom_q50 > izip_encoding GR_ZOOM_Q50;
/* GR_ZOOM_Q90
* 90th quantile values for 100bp segments of the graph chunk
*/
extern column < NCBI:SeqGraph:gr_zoom_q90 > izip_encoding GR_ZOOM_Q90;
/* GR_ZOOM_Q100
* Maximal values for 100bp segments of the graph chunk
*/
extern column < NCBI:SeqGraph:gr_zoom_q100 > izip_encoding GR_ZOOM_Q100;
/* NUM_SWITCHES
* Number of value switches within the graph. Helps client make the decision how better to
* represent the graph in ASN.1 (Seq-graph or Seq-table).
*/
extern column < NCBI:SeqGraph:gr_num_switches > izip_encoding NUM_SWITCHES;
};
database NCBI:SeqGraph:database:kmergraph #1.0
{
table NCBI:SeqGraph:tbl:seqgraph #1.0 LEFT;
table NCBI:SeqGraph:tbl:seqgraph #1.0 RIGHT;
table NCBI:SeqGraph:tbl:seqgraph #1.0 SUM;
}
|