/usr/lib/ncbi-vdb/ncbi/stats.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 | /*===========================================================================
*
* 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/insdc/sra.vschema';
/*--------------------------------------------------------------------------
* types
*/
typeset NCBI:SRA:stats:qual_type
{
INSDC:quality:phred,
INSDC:quality:log_odds,
INSDC:quality:log_odds [ 4 ]
};
/*--------------------------------------------------------------------------
* functions
*/
/*
trigger to build meta statistics: spot count, base count, etc.
*/
extern function U8 NCBI:SRA:stats_trigger #1
( U8 read_bin, U32 read_len, INSDC:SRA:xread_type read_type * ascii spot_group );
/* trigger to build meta statistics from compressed reads
*/
extern function
U8 NCBI:SRA:cmp_stats_trigger #1 ( B8 cmp_read_bin, NCBI:SRA:stats:qual_type qual_bin,
U32 read_len, INSDC:SRA:xread_type read_type * ascii spot_group );
extern function
U8 NCBI:SRA:cmpf_stats_trigger #1 ( B8 cmp_read_bin, U32 spot_len,
U32 read_len, INSDC:SRA:xread_type read_type * ascii spot_group );
/* trigger to build phred_quality statistics in meta
*/
extern function
U8 NCBI:SRA:phred_stats_trigger #1 ( INSDC:quality:phred qual_bin );
/*--------------------------------------------------------------------------
* table
*/
/* stats
* holds sequence statistics
*
* history:
* 1.0.1 - explicitly interit from sra #1.0.1
* 1.1.0 - incorporate stats from compressed read
* 1.1.1 - sra #1.0.2
* 1.1.2 - sra #1.0.3 + cmp_base_count or to base_count
*/
table NCBI:SRA:tbl:stats #1.2.0 = INSDC:SRA:tbl:stats #1.1, INSDC:SRA:tbl:sra #1.0.3
{
INSDC:SRA:spotid_t min_spot_id
= < INSDC:SRA:spotid_t > meta:value < "STATS/TABLE/SPOT_MIN" > ();
INSDC:SRA:spotid_t max_spot_id
= < INSDC:SRA:spotid_t > meta:value < "STATS/TABLE/SPOT_MAX" > ();
U64 spot_count
= < U64 > meta:value < "STATS/TABLE/SPOT_COUNT" > ();
U64 base_count
= < U64 > meta:value < "STATS/TABLE/BASE_COUNT" > ();
U64 bio_base_count
= < U64 > meta:value < "STATS/TABLE/BIO_BASE_COUNT" > ();
U64 cmp_base_count
= < U64 > meta:value < "STATS/TABLE/CMP_BASE_COUNT" > () | base_count;
trigger meta_stats
= NCBI:SRA:stats_trigger ( in_stats_bin, in_read_len, in_read_type, in_spot_group )
| NCBI:SRA:stats_trigger ( in_stats_bin, in_read_len, in_read_type )
| NCBI:SRA:cmp_stats_trigger ( in_cmp_stats_bin, in_stats_qual, in_read_len, in_read_type, in_spot_group )
| NCBI:SRA:cmp_stats_trigger ( in_cmp_stats_bin, in_stats_qual, in_read_len, in_read_type )
| NCBI:SRA:cmpf_stats_trigger ( in_cmp_stats_bin, in_spot_len, in_read_len, in_read_type, in_spot_group )
| NCBI:SRA:cmpf_stats_trigger ( in_cmp_stats_bin, in_spot_len, in_read_len, in_read_type );
trigger qual_stats
= NCBI:SRA:phred_stats_trigger #1 ( in_qual_phred );
/* INSDC:SRA:tbl:stats inherited virtual productions
* in_stats_bin
*/
};
|