/usr/lib/ncbi-vdb/csra2/stats.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.
*
* ===========================================================================
*
*/
/*==========================================================================
* NCBI Sequence Read Archive schema
*/
version 1;
include '/usr/lib/ncbi-vdb/vdb/vdb.vschema';
include '/usr/lib/ncbi-vdb/insdc/insdc.vschema';
include '/usr/lib/ncbi-vdb/insdc/sra.vschema';
/*--------------------------------------------------------------------------
* functions
*/
extern function
U8 NCBI:csra2:stats_trigger #1 ( B8 read_bin * ascii read_group );
extern function
U8 NCBI:csra2:phred_stats_trigger #1 ( INSDC:quality:phred qual_bin )
= NCBI:SRA:phred_stats_trigger;
/*--------------------------------------------------------------------------
* table
*/
table NCBI:csra2:tbl:read_stats #1
{
readonly column I64 MIN_READ_ID = min_read_id;
readonly column I64 MAX_READ_ID = max_read_id;
readonly column U64 READ_COUNT = read_count;
readonly column U64 BASE_COUNT = base_count;
/* introduce compatibility names */
readonly column INSDC:SRA:spotid_t MIN_SPOT_ID = cast ( min_read_id );
readonly column INSDC:SRA:spotid_t MAX_SPOT_ID = cast ( max_read_id );
readonly column U64 SPOT_COUNT = read_count;
/* reading rules */
I64 min_read_id
= < I64 > meta:value < "STATS/TABLE/READ_MIN" > ()
| < I64 > meta:value < "STATS/TABLE/SPOT_MIN" > ()
| < I64 > echo < 1 > ()
;
I64 max_read_id
= < I64 > meta:value < "STATS/TABLE/READ_MAX" > ()
| < I64 > meta:value < "STATS/TABLE/SPOT_MAX" > ()
| cast ( read_count )
;
U64 read_count
= < U64 > meta:value < "STATS/TABLE/READ_COUNT" > ()
| < U64 > meta:value < "STATS/TABLE/SPOT_COUNT" > ()
;
U64 base_count
= < U64 > meta:value < "STATS/TABLE/BASE_COUNT" > ()
;
/* triggers */
trigger meta_stats
= NCBI:csra2:stats_trigger ( in_stats_seq, in_stats_read_group )
| NCBI:csra2:stats_trigger ( in_stats_seq )
;
trigger qual_stats
= NCBI:csra2:phred_stats_trigger #1 ( in_stats_qual_phred )
;
}
|