sra-toolkit 2.1.7a-1ubuntu2 / usr / lib / ncbi / schema / illumina.vschema

/*===========================================================================
*
*                            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 Illumina Sequence Read Archive schema
 */
version 1;

include 'ncbi/sra.vschema';
include 'ncbi/spotname.vschema';


/*--------------------------------------------------------------------------
 * types
 */

typedef INSDC:quality:log_odds NCBI:qual4 [ 4 ];
typedef NCBI:qual4 NCBI:SRA:rotated_qual4, NCBI:SRA:swapped_qual4;


/*--------------------------------------------------------------------------
 * functions
 */

/* tokenize_spot_name
 *  scans name on input
 *  tokenizes into parts
 */
extern function NCBI:SRA:spot_name_token
    NCBI:SRA:Illumina:tokenize_spot_name #1 ( ascii name );


/*--------------------------------------------------------------------------
 * NCBI:SRA:Illumina:qual4
 *  4-channel log-odds-ish quality
 */

/* history:
 *  1.0.1 - base explicitly upon updated ancestry
 */
table NCBI:SRA:Illumina:qual4_nocol #1.0.1
    = INSDC:tbl:sequence #1.0.1
    , NCBI:tbl:log_odds_quality_nocol #1.0.1
{
    /* QUALITY
     *  4-channel quality column
     */
    readonly column NCBI:qual4 QUALITY = out_qual4;

    NCBI:qual4 out_qual4
        = < NCBI:qual4 > NCBI:SRA:swap ( out_qual4_swapped, read_unpack )
        | < NCBI:qual4 > NCBI:SRA:rotate < false > ( out_qual4_rotated, read_unpack );


    /* single-channel output
     *  convert 4-channel log-odds to single channel
     *  must retain n-encoding, which was intended to be the 4-channel pattern
     *  ( -5, -5, -5, -5 ) and a base of 'A'
     */

    // first, extract quality for called base
    INSDC:quality:log_odds out_qual1_ch0
        = < INSDC:quality:log_odds> cut < 0 > ( out_qual4_swapped )
        | < INSDC:quality:log_odds> cut < 0 > ( out_qual4_rotated );

    // clip it to -5 and above
    INSDC:quality:log_odds out_qual1_clip
        = < INSDC:quality:log_odds > clip < -5, 127 > ( out_qual1_ch0 );

    // convert 4 channel to single 32-bit value
    U32 out_qual4_32
        = redimension ( out_qual4_swapped )
        | redimension ( out_qual4_rotated );

    // detect ( -5, -5, -5, -5 ) and introduce a -6 value into log-odds
    // this is treated as an 'N', but still not ready
    INSDC:quality:log_odds out_qual1_fives
        = < U32, INSDC:quality:log_odds > map < 0xFBFBFBFB, -6 > ( out_qual4_32, out_qual1_clip );

    // now slam zeros into anything that doesn't correspond to an A
    // essentially this leaves all of the A qualities. any having -6 are really N.
    INSDC:quality:log_odds out_qual1_n
        = < U8, INSDC:quality:log_odds > map < [ 1, 2, 3 ], [ 0, 0, 0 ] > ( read_unpack, out_qual1_fives );

    // finally, produce log-odds with n-encoded as -6
    INSDC:quality:log_odds out_qual_log_odds
        = < INSDC:quality:log_odds, INSDC:quality:log_odds > map < -6, -6 > ( out_qual1_n, out_qual1_clip );


	/* NCBI:tbl:n_encoding inherited productions
	 *  read_unpack
	 */

	/* NCBI:SRA:Illumina:qual4_nocol productions
	 *  out_qual4_rotated
	 *  out_qual4_swapped
	 */
};


/* 4-channel log-odds compression
 */

// encoded type - a single byte code for 4-channel pattern
typedef B8 NCBI:SRA:encoded_qual4;

// decoding function
extern function
NCBI:SRA:swapped_qual4 NCBI:SRA:qual4_decode #1 ( NCBI:SRA:encoded_qual4 in );

// encoding function
extern function
NCBI:SRA:encoded_qual4 NCBI:SRA:qual4_encode #1 ( NCBI:SRA:swapped_qual4 in );

// compression rules
physical NCBI:SRA:swapped_qual4 NCBI:SRA:qual4_encoding #1
{
    encode
    {
        // produce codes
        NCBI:SRA:encoded_qual4 encoded = NCBI:SRA:qual4_encode ( @ );

        // gzip
        return zip < Z_RLE, Z_BEST_SPEED > ( encoded );
    }

    decode
    {
        // gunzip
        NCBI:SRA:encoded_qual4 unzipped = unzip ( @ );
        
        // inflate to swapped
        return NCBI:SRA:qual4_decode ( unzipped );
    }
}

/* history:
 *  1.0.1 - base upon updated qual4_nocol
 */
table NCBI:SRA:Illumina:qual4 #1.0.1 = NCBI:SRA:Illumina:qual4_nocol #1.0.1
{
    // read directly as swapped, n-encoded log_odds
    NCBI:SRA:swapped_qual4 out_qual4_swapped = .QUALITY;

	/* NCBI:tbl:n_encoding inherited virtual productions
	 *  read_unpack
	 */
};

/* history:
 *  2.0.2 - base upon updated ancestry
 *  2.0.3 - base upon updated ancestry
 *  2.0.4 - base upon updated ancestry
 */
table NCBI:SRA:Illumina:qual4 #2.0.4
    = NCBI:tbl:base_space #2.0.3
    , NCBI:tbl:log_odds_quality_nocol #2.0.1
{
    /* QUALITY
     *  4-channel log-odds
     */
    extern column NCBI:qual4 QUALITY = out_qual4;

    NCBI:SRA:swapped_qual4 in_qual4
        = ( NCBI:SRA:swapped_qual4 ) < NCBI:qual4 > NCBI:SRA:swap ( QUALITY, in_x2na_bin )
        | ( NCBI:SRA:swapped_qual4 ) < NCBI:qual4 > NCBI:SRA:swap ( QUALITY, in_2na_bin );

    NCBI:qual4 out_qual4
        = < NCBI:SRA:swapped_qual4 > NCBI:SRA:swap ( .QUALITY, out_x2na_bin );

    physical column NCBI:SRA:qual4_encoding .QUALITY = in_qual4;

    // feed to compressed statistics
    NCBI:qual4 in_stats_qual = in_qual4;

    // single channel
    INSDC:quality:log_odds out_qual_log_odds
        = < INSDC:quality:log_odds > cut < 0 > ( .QUALITY );
};


/*--------------------------------------------------------------------------
 * NCBI:SRA:Illumina
 *  Illumina SRA Platform
 */


/* NCBI:SRA:Illumina:common #1
 *  basic table interface based upon Illumina's pipelines
 *
 * history:
 *  1.0.1 - explictly base upon sra #1.0.1
 *  1.0.2 - base explicitly upon sra #1.0.2
 *  1.0.3 - base explicitly upon sra #1.0.3
 */
table NCBI:SRA:Illumina:common #1.0.3 = INSDC:SRA:tbl:sra #1.0.3
{
    // platform name is always 'ILLUMINA'
    ascii platform_name
        = < ascii > echo < "ILLUMINA" > ();

    /* TRIMMED SEQUENCE
     *  need to find the 0-based trim_start and trim_len
     */
    INSDC:coord:zero bio_start = NCBI:SRA:bio_start ( out_read_start, out_read_type );
    INSDC:coord:zero trim_start = bio_start;
    U32 trim_left = ( U32 ) trim_start;
    INSDC:coord:len trim_len = (INSDC:coord:len) < U32 > diff ( spot_len, trim_left );

    /* COORDINATES
     *  in addition to X and Y,
     *  Illumina has LANE and TILE
     */
    readonly column INSDC:coord:val LANE = out_lane_coord;
    readonly column INSDC:coord:val TILE = out_tile_coord;
};


/*--------------------------------------------------------------------------
 * NCBI:SRA:Illumina:tbl:v2 #1
 *  normalized v2 table
 *  still has variants based upon quality type
 *
 * history:
 *  1.0.1 - explictly base upon sra #1.0.1 and related tables
 *  1.0.2 - updated ancestry
 *  1.0.3 - updated ancestry
 */

physical NCBI:SRA:swapped_fsamp4 NCBI:SRA:Illumina:encoding:SIGNAL #2
{
    decode { return NCBI:SRA:fsamp4:decode #2 ( @ ); }
    encode { return NCBI:SRA:fsamp4:encode #2 < 14, 10 > ( @ ); }
}

physical NCBI:fsamp4 NCBI:SRA:Illumina:encoding:NOISE #2
{
    decode
    {
        F32 dcmp = funzip ( @ );
        return redimension ( dcmp );
    }
    encode
    {
	F32 ncmp = redimension ( @ );
        return fzip < 10 > ( ncmp );
    }
}

physical NCBI:SRA:swapped_fsamp4 NCBI:SRA:Illumina:encoding:INTENSITY #2
{
    decode { return NCBI:SRA:fsamp4:decode #2 ( @ ); }
    encode { return NCBI:SRA:fsamp4:encode #2 < 14, 10 > ( @ ); }
}

// v2 base table
table NCBI:SRA:Illumina:tbl:v2 #1.0.4
    = NCBI:SRA:tbl:sra #2.1.3
    , NCBI:tbl:base_space #2.0.3
    , NCBI:SRA:Illumina:common #1.0.3
{
    /* NAME tokenizing and coordinates
     *  most work happens in skeyname table
     *  we still obtain LANE and TILE from name
     */
    INSDC:coord:val out_lane_coord = ( INSDC:coord:val )
        NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:L > ( _out_name, out_spot_name_tok );
    INSDC:coord:val out_tile_coord = ( INSDC:coord:val )
        NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:T > ( _out_name, out_spot_name_tok );
    NCBI:SRA:spot_name_token out_spot_name_tok
        = NCBI:SRA:Illumina:tokenize_spot_name ( _out_name );

    NCBI:SRA:spot_name_token in_spot_name_tok
        = NCBI:SRA:Illumina:tokenize_spot_name ( NAME );

    /* SIGNAL
     *  optional, no longer archived
     */
    extern column NCBI:fsamp4 SIGNAL
    {
        read = out_signal;
        validate = < NCBI:fsamp4 > no_compare #1 ( in_signal, out_signal );
    }
    NCBI:fsamp4 in_signal = SIGNAL;
    NCBI:fsamp4 out_signal
        = < NCBI:SRA:swapped_fsamp4 > NCBI:SRA:swap ( .SIGNAL, out_x2na_bin );

    physical column NCBI:SRA:Illumina:encoding:SIGNAL #2 .SIGNAL
        = ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_signal, in_x2na_bin )
        | ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_signal, in_2na_bin );

    /* NOISE
     *  optional, no longer archived
     */
    extern column NCBI:fsamp4 NOISE
    {
        read = out_noise;
        validate = < NCBI:fsamp4 > no_compare #1 ( in_noise, out_noise );
    }
    NCBI:fsamp4 in_noise = NOISE;
    NCBI:fsamp4 out_noise = .NOISE;

    physical column NCBI:SRA:Illumina:encoding:NOISE #2 .NOISE = in_noise;

    /* INTENSITY
     *  optional, no longer archived
     */
    extern column NCBI:fsamp4 INTENSITY
    {
        read = out_intensity;
        validate = < NCBI:fsamp4 > no_compare #1 ( in_intensity, out_intensity );
    }
    NCBI:fsamp4 in_intensity = INTENSITY;
    NCBI:fsamp4 out_intensity
        = < NCBI:fsamp4 > NCBI:SRA:denormalize ( out_norm_intensity, out_x2na_bin );
    NCBI:fsamp4 out_norm_intensity
        = ( NCBI:fsamp4 ) < NCBI:SRA:swapped_fsamp4 > NCBI:SRA:swap ( .INTENSITY, out_x2na_bin );
    NCBI:fsamp4 in_norm_intensity
        = < NCBI:fsamp4 > NCBI:SRA:normalize ( in_intensity, in_x2na_bin )
        | < NCBI:fsamp4 > NCBI:SRA:normalize ( in_intensity, in_2na_bin );
    physical column NCBI:SRA:Illumina:encoding:INTENSITY #2 .INTENSITY
        = ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_norm_intensity, in_x2na_bin )
        | ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_norm_intensity, in_2na_bin );

	/* INSDC:tbl:sequence inherited virtual productions
	 *  out_qual_phred
	 */

	/* INSDC:SRA:tbl:spotdesc inherited productions
	 *  static_fixed_spot_len
	 */
};

/* 4-channel log-odds qualities
 *
 * history:
 *  1.0.2 - updated ancestry
 *  1.0.3 - updated ancestry
 *  1.0.4 - updated ancestry
 */
table NCBI:SRA:Illumina:tbl:q4:v2 #1.0.4
    = NCBI:SRA:Illumina:tbl:v2 #1.0.4
    , NCBI:SRA:Illumina:qual4 #2.0.4
{
	/* INSDC:SRA:tbl:spotdesc inherited virtual productions
	 *  static_fixed_spot_len
	 */
};

/* 1-channel log-odds qualities
 *
 * history:
 *  1.0.2 - updated ancestry
 *  1.0.3 - updated ancestry
 *  1.0.4 - updated ancestry
 */
table NCBI:SRA:Illumina:tbl:q1:v2 #1.0.4
    = NCBI:SRA:Illumina:tbl:v2 #1.0.4
    , NCBI:tbl:log_odds_quality #2.0.3
{
	/* INSDC:SRA:tbl:spotdesc inherited productions
	 *  static_fixed_spot_len
	 */
};

/* phred qualities
 *
 * history:
 *  1.0.2 - updated ancestry
 *  1.0.3 - updated ancestry
 *  1.0.4 - updated ancestry
 */
table NCBI:SRA:Illumina:tbl:phred:v2 #1.0.4
    = NCBI:SRA:Illumina:tbl:v2 #1.0.4
    , NCBI:tbl:phred_quality #2.0.3
{
	/* INSDC:SRA:tbl:spotdesc inherited virtual productions
	 *  static_fixed_spot_len
	 */
};