This file is indexed.

/usr/lib/ncbi-vdb/align/refseq.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
/*===========================================================================
*
*                            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;