/usr/lib/ncbi-vdb/ncbi/seq-graph.vschema is in libncbi-vdb2 2.8.1+dfsg-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.
*
* ===========================================================================
*
*/
/*==========================================================================
* 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;
}
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