/*===========================================================================
*
*                            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 'vdb/vdb.vschema';
include 'ncbi/seq.vschema';
include 'ncbi/sra.vschema';
include '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 #2 =
    NCBI:tbl:base_space #3,
    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;