/usr/lib/ncbi-vdb/align/refseq.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.
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 | /*===========================================================================
*
* 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.
*
* ===========================================================================
*
*/
/*==========================================================================
* VDB Reference Sequence types, functions and tables
*/
version 1;
include '/usr/lib/ncbi-vdb/vdb/vdb.vschema';
include '/usr/lib/ncbi-vdb/ncbi/seq.vschema';
include '/usr/lib/ncbi-vdb/ncbi/sra.vschema';
include '/usr/lib/ncbi-vdb/ncbi/stats.vschema';
extern function U8 NCBI:refseq:stats #2 ( INSDC:4na:bin seq, INSDC:coord:len len )
= NCBI:refSeq:stats;
table NCBI:refseq:tbl:reference #1.0.2 =
NCBI:tbl:base_space #2.0.2,
NCBI:tbl:phred_quality #2.0.3,
NCBI:tbl:seqloc #1.0,
NCBI:SRA:tbl:stats #1.1.2
{
// 128K
column default limit = 131072;
extern column U32 MAX_SEQ_LEN; /* must be static */
extern column < ascii > izip_encoding DEF_LINE; /* remainder of defline after SEQ_ID */
// trigger upconverts to INSDC:dna:text to get MD5
trigger table_stats
= NCBI:refseq:stats(in_4na_bin, _alt_in_read_len);
readonly column U64 TOTAL_SEQ_LEN
= < U64 > meta:value < 'STATS/TOTAL_SEQ_LEN', true >();
readonly column U8[16] MD5
= < U8[16] > meta:read < 'STATS/MD5', true >();
// indicates if sequence has circular structure
// should be static
extern column bool_encoding CIRCULAR;
/* columns:
* READ
* QUALITY (optional)
* SEQ_ID
* SEQ_START
* SEQ_LEN
* MAX_SEQ_LEN
* TOTAL_SEQ_LEN
* DEF_LINE
*/
// make CS_KEY writable
INSDC:dna:text in_cs_key
= < INSDC:dna:text, INSDC:dna:text > map < 'acgtn', 'ACGTN' > ( CS_KEY );
physical column < INSDC:dna:text > zip_encoding .CS_KEY = in_cs_key;
// extra columns needed for CS conversion
INSDC:coord:zero out_read_start = < INSDC:coord:zero> echo < 0 > ();
INSDC:coord:len out_read_len = .SEQ_LEN;
INSDC:coord:len _alt_in_read_len
= READ_LEN
| SEQ_LEN;
INSDC:SRA:xread_type _alt_in_read_type
= READ_TYPE
| < INSDC:SRA:xread_type > echo < SRA_READ_TYPE_BIOLOGICAL > ();
INSDC:SRA:xread_type out_read_type
= .READ_TYPE
| < INSDC:SRA:xread_type > echo < SRA_READ_TYPE_BIOLOGICAL > ();
};
// older spelling
alias NCBI:refseq:tbl:reference NCBI:refSeq:tbl:reference;
|