Mercurial > repos > charles_s_test > seqsero2

/*===========================================================================
*
*                            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 'vdb/vdb.vschema';
include 'insdc/insdc.vschema';
include '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 )
        ;
}
author	charles_s_test
date	Mon, 27 Nov 2017 11:21:07 -0500
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