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 'ncbi/seq.vschema';
include 'ncbi/spotname.vschema';
include 'insdc/sra.vschema';
include 'ncbi/stats.vschema';


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


/* Segment - DEPRECATED
 *  a ( start, len ) pair where start is a zero-based, unsigned coordinate
 */
typedef U16 NCBI:SRA:Segment [ 2 ];


/* SpotDesc - DEPRECATED
 *   uint16_t spot_len;
 *   uint16_t fixed_len;
 *   uint16_t signal_len;
 *   uint16_t clip_qual_right;
 *   uint8_t num_reads;
 *   uint8_t align [ 7 ];
 */
typedef B8 NCBI:SRA:SpotDesc [ 16 ];


/* ReadDesc - DEPRECATED
 *   SRASegment { uint16_t start, len; } seg;
 *   uint8_t type;
 *   char cs_key;
 *   char label [ 74 ];
 */
typedef B8 NCBI:SRA:ReadDesc [ 80 ];


// some types have been moved to INSDC
alias INSDC:SRA:platform_id NCBI:SRA:platform_id;
alias INSDC:SRA:read_type NCBI:SRA:read_type;
alias INSDC:SRA:read_filter NCBI:SRA:read_filter;

typedef NCBI:fsamp4 NCBI:SRA:rotated_fsamp4, NCBI:SRA:swapped_fsamp4;

// 16-bit POSITION type
typedef U16 NCBI:SRA:pos16;


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

/* bio_start
 *  searches through read_type vector
 *  returns the 0-based starting coordinate of first biological read
 *
 *  "read_start" [ DATA ] - vector of read start coordinates
 *
 *  "read_type" [ DATA ] - vector of read types
 */
extern function INSDC:coord:zero
    NCBI:SRA:bio_start #1 ( INSDC:coord:zero read_start, INSDC:SRA:xread_type read_type );


/* bio_end
 *  searcehes through read_type vector
 *  returns the 0 based ending coording (either inclusive or exclusive) of last
 *  biological read
 *
 *  "read_start" [ DATA ] - vector of read start coordinates
 *
 *  "read_type" [ DATA ] - vector of read types
 *
 *  "read_len" [ DATA ] - vector of read lengths
 */
extern function INSDC:coord:zero
    NCBI:SRA:bio_end #1 < bool inclusive > ( INSDC:coord:zero read_start, INSDC:SRA:xread_type read_type, INSDC:coord:len read_len );


/* fix_read_seg
 */
extern function INSDC:coord:len [ 2 ]
    NCBI:SRA:fix_read_seg #1 ( U16 [ 2 ] rd_seg, INSDC:coord:len spot_len );


/* make_spot_desc
 *  assembles several bits of information together into a "C" structure
 *
 *  "spot_len" [ DATA ] - computed spot length value
 *
 *  "fixed_len" [ DATA, DFLT ZERO ] - the stated fixed length of all spots
 *  or zero if not fixed length
 *
 *  "sig_len" [ DATA, DFLT ZERO ] - the length of signal/intensity data
 *  or zero if not present
 *
 *  "trim_start" [ DATA ] - the first base included in the trim segment
 *
 *  "trim_len" [ DATA ] - the length of the trim segment
 *
 *  "num_reads" [ DATA ] - 1..n value
 */
extern function NCBI:SRA:SpotDesc NCBI:SRA:make_spot_desc #1 ( INSDC:coord:len spot_len,
    INSDC:coord:len fixed_len,  INSDC:coord:len sig_len, INSDC:coord:zero trim_start,
    INSDC:coord:len trim_len, U8 num_reads );


/* make_read_desc
 *  assembles several bits of information together into a "C" structure
 *  in theory resultant segments may intersect other read segments or leave holes in spot.
 *
 *  "num_reads" [ DATA ] - value indicating the resulting row-length of output
 *
 *  "read_start" [ DATA ] - ordered starting coordinates for each read
 *  not required to be sequential.
 *
 *  "read_len" [ DATA ] - ordered lengths of each read. may be zero when
 *  read has been described but is not identified in spot.
 *
 *  "read_type" [ DATA ] - ordered type id describing each read
 *
 *  "read_filt" [ DATA ] - ordered read filters
 *
 *  "cs_key" [ DATA ] - ordered color-space keys
 *
 *  "label_start" [ DATA ] - ordered starting coordinates for each label
 *  "label_len" [ DATA ] - ordered lengths of each label
 *
 *  "label" [ DATA ] - complete sequence of label characters, possibly empty
 *  individual read labels are identified as {start,len} pairs
 */
extern function NCBI:SRA:ReadDesc NCBI:SRA:make_read_desc #1 ( U8 num_reads,
    INSDC:coord:zero read_start, INSDC:coord:len read_len, INSDC:SRA:xread_type read_type,
    INSDC:SRA:read_filter read_filt, INSDC:dna:text cs_key,
    INSDC:coord:zero label_start, INSDC:coord:len label_len, ascii label );


/* rotate
 *  rotate a quadruple by called base
 *  now normally replaced by swap
 *
 *  "T" [ TYPE ] - element type of quadruple to be rotated
 *
 *  "encoding" [ CONST ] - when true, rotate input left until corresponding
 *  element is in slot 0. when false, rotate input right to restore original
 *  order.
 *
 *  "in" [ DATA ] - data to be rotated, qualities, signal, intensities...
 *
 *  "called" [ DATA ] - {0..3} or {0..4} binary representation of called bases or colors
 */
extern function < type T >
T NCBI:SRA:rotate #1 < bool encoding > ( T in, U8 called );


/* swap
 *  swap element 0 and the called element
 *  used to ensure that the called element is in slot 0
 *
 *  "T" [ TYPE ] - element type of quadruple to be swapped
 *
 *  "in" [ DATA ] - data to be swapped, qualities, signal, intensities...
 *
 *  "called" [ DATA ] - {0..3} or {0..4} binary representation of called bases or colors
 */
extern function < type T >
T NCBI:SRA:swap #1 ( T in, U8 called );


/* normalize
 * denormalize
 *
 *  "T" [ TYPE ] - element type of quadruple to be [de]normalized
 *
 *  "intensity" [ DATA ] - intensity data
 *
 *  "called" [ DATA ] - {0..3} or {0..4} binary representation of called bases or colors
 */
extern function < type T >
T NCBI:SRA:normalize #1 ( T intensity, U8 called );

extern function < type T >
T NCBI:SRA:denormalize #1 ( T intensity, U8 called );


/* make_position
 *  return a synthesized position row with 1-1 correspondence
 *
 *  "T" [ TYPE ] - position type being generated
 *
 *  "start" [ CONST ] - either 0 or 1, depending upon the coordinate system
 *
 *  "bases" [ DATA ] - the actual row of bases. the output row
 *  will be the same length, but with synthesized data
 */
extern function < type T >
T NCBI:SRA:make_position #1 < T start > ( any bases );

/* fsamp4 compression
 *  performs compression individually
 *  on called channel and alternate channels
 */
function NCBI:SRA:swapped_fsamp4 NCBI:SRA:fsamp4:decode #2 ( merged_fmt in )
{
    fzip_fmt cmp0 = split < 0 > ( in );
    fzip_fmt cmp123 = split < 1 > ( in );
    F32 ch0 = funzip ( cmp0 );
    F32 ch123a = funzip ( cmp123 );
    F32[3] ch123 = redimension ( ch123a );
    return ( NCBI:SRA:swapped_fsamp4 ) < F32 > paste ( ch0, ch123 );
}

function merged_fmt NCBI:SRA:fsamp4:encode #2 < U32 called, U32 alt > ( NCBI:SRA:swapped_fsamp4 in )
{
    F32 ch0 = < F32 > cut < 0 > ( in );
    F32[3] ch123 = < F32 > cut < 1, 2, 3 > ( in );
    fzip_fmt cmp0 = fzip < called > ( ch0 );
    F32 ch123a = redimension ( ch123 );
    fzip_fmt cmp123 = fzip < alt > ( ch123a );
    return merge ( cmp0, cmp123 );
}


/*--------------------------------------------------------------------------
 * spotdesc
 *  NCBI implementation productions
 */

/* history:
 *  1.0.1 - base explicitly upon sequence #1.0.1, spotdesc #1.0.1
 *  1.0.2 - spotdesc #1.0.2
 */
table NCBI:SRA:tbl:spotdesc_nocol #1.0.2 = INSDC:tbl:sequence #1.0.1, INSDC:SRA:tbl:spotdesc #1.0.2
{
    /* LABEL_SEG
     */
    readonly column NCBI:SRA:Segment LABEL_SEG
        = out_label_seg
        | cast ( out_label_seg32 )
        | cast ( _out_label_seg32 );
    U32 _out_label_startU32 = ( U32 ) out_label_start;
    U32 [ 2 ] _out_label_seg32 = < U32 > paste ( _out_label_startU32, out_label_len );


    /* READ_SEG
     */
    readonly column NCBI:SRA:Segment READ_SEG
        = out_read_seg
        | cast ( out_read_seg32 )
        | cast ( _out_read_seg32 );
    U32 _out_read_startU32 = ( U32 ) out_read_start;
    U32 [ 2 ] _out_read_seg32 = < U32 > paste ( _out_read_startU32, out_read_len );


    /* READ_DESC
     */
    readonly column NCBI:SRA:ReadDesc READ_DESC
        = NCBI:SRA:make_read_desc ( out_nreads, out_read_start, out_read_len,
              out_read_type, _out_rd_filter, out_cs_key, _out_label_start, _out_label_len, _out_label );
    INSDC:SRA:read_filter _out_rd_filter
        = out_rd_filter
        | < INSDC:SRA:read_filter > echo < SRA_READ_FILTER_PASS > ( out_read_start );
    ascii _out_label
        = out_label
        | < ascii > echo < '' > ();
    INSDC:coord:zero _out_label_start
        = out_label_start
        | < INSDC:coord:zero > echo < 0 > ( out_read_start );
    INSDC:coord:len _out_label_len
        = out_label_len
        | < INSDC:coord:len > echo < 0 > ( out_read_start );

    /* SPOT_DESC
     */
    readonly column NCBI:SRA:SpotDesc SPOT_DESC
        = NCBI:SRA:make_spot_desc ( spot_len, fixed_spot_len, signal_len,
              trim_start, trim_len, out_nreads );

    /* SIGNAL_LEN
     *  normally the same as spot length when present,
     *  but in some cases ( e.g. 454 ) it may be different
     */
    readonly column INSDC:coord:len SIGNAL_LEN
        = signal_len;
    readonly column U16 SIGNAL_LEN
        = cast ( signal_len );


	/* INSDC:SRA:tbl:spotdesc inherited productions
	 *  trim_len
	 *  out_label
	 *  out_nreads
	 *  trim_start
	 *  out_read_len
	 *  out_label_len
	 *  out_rd_filter
	 *  out_read_type
	 *  out_read_start
	 *  out_label_start
	 *  static_fixed_spot_len
	 */

	/* NCBI:SRA:tbl:spotdesc_nocol productions
	 *  out_read_seg
	 *  out_label_seg
	 *  out_read_seg32
	 *  out_label_seg32
	 */
};

/* history:
 *  1.0.1 - base explicitly upon spotdesc_nocol #1.0.1
 *  1.0.2 - base explicitly upon spotdesc_nocol #1.0.2
 */
table NCBI:SRA:tbl:spotdesc_nophys #1.0.2 = NCBI:SRA:tbl:spotdesc_nocol #1.0.2
{
    // resolve virtual productions
    U8 out_nreads = .NREADS;
    ascii out_label = .LABEL;
    INSDC:SRA:xread_type out_read_type = .READ_TYPE;
    INSDC:SRA:read_filter out_rd_filter  = .RD_FILTER;

    INSDC:coord:zero out_label_start
        = .LABEL_START
        | ( INSDC:coord:zero ) < U32 > cut < 0 > ( out_label_seg32 );
    INSDC:coord:len out_label_len
        = .LABEL_LEN
        | ( INSDC:coord:len ) < U32 > cut < 1 > ( out_label_seg32 );
    U32 [ 2 ] out_label_seg32
        = cast ( .LABEL_SEG );

    INSDC:coord:zero out_read_start
        = .READ_START
        | ( INSDC:coord:zero ) < U32 > cut < 0 > ( out_read_seg32 );
    INSDC:coord:len out_read_len
        = .READ_LEN
        | ( INSDC:coord:len ) < U32 > cut < 1 > ( out_read_seg32 );
    U32 [ 2 ] out_read_seg32
        = NCBI:SRA:fix_read_seg ( .READ_SEG, spot_len );


	/* INSDC:SRA:tbl:spotdesc inherited productions
	 *  trim_len
	 *  trim_start
	 *  out_read_type
	 *  static_fixed_spot_len
	 */

	/* NCBI:SRA:tbl:spotdesc_nocol inherited productions
	 *  out_read_seg
	 *  out_label_seg
	 */

	/* NCBI:SRA:tbl:spotdesc_nophys productions
	 *  .LABEL
	 *  .NREADS
	 *  .READ_LEN
	 *  .READ_SEG
	 *  .LABEL_LEN
	 *  .LABEL_SEG
	 *  .RD_FILTER
	 *  .READ_TYPE
	 *  .READ_START
	 *  .LABEL_START
	 */
}

/* history:
 *  1.0.1 - base explicitly upon spotdesc_nophys #1.0.1
 *  1.0.2 - base explicitly upon spotdesc_nophys #1.0.2
 */
table NCBI:SRA:tbl:spotdesc #1.0.2 = NCBI:SRA:tbl:spotdesc_nophys #1.0.2
{
    // physical column encodings
    // TBD - this has to be looked at, where dynamic segmentation is involved
    physical column < U8 > zip_encoding .NREADS = NREADS;
    physical column < ascii > zip_encoding .LABEL = LABEL;
    physical column < INSDC:coord:zero > izip_encoding .LABEL_START = LABEL_START;
    physical column < INSDC:coord:len > izip_encoding .LABEL_LEN = LABEL_LEN;
    physical column < INSDC:coord:zero > izip_encoding .READ_START = READ_START;
    physical column < INSDC:coord:len > izip_encoding .READ_LEN = in_read_len;
    physical column < INSDC:SRA:xread_type > zip_encoding .READ_TYPE = in_read_type;
    physical column < INSDC:SRA:read_filter > zip_encoding .RD_FILTER = READ_FILTER;


	/* INSDC:SRA:tbl:spotdesc inherited productions
	 *  trim_len
	 *  trim_start
	 *  out_read_type
	 *  static_fixed_spot_len
	 */

	/* NCBI:SRA:tbl:spotdesc_nocol inherited productions
	 *  out_read_seg
	 *  out_label_seg
	 */
};


/*--------------------------------------------------------------------------
 * pos
 *  synthetic POSITION column on read
 *
 * history:
 *  1.0.1 - base explicitly upon sequence #1.0.1
 */

table NCBI:SRA:tbl:pos #1.0.1 = INSDC:tbl:sequence #1.0.1
{
    INSDC:position:one out_position
        = < INSDC:position:one > NCBI:SRA:make_position < 1 > ( out_2na_packed )
        | < INSDC:position:one > NCBI:SRA:make_position < 1 > ( out_2cs_packed );
    NCBI:SRA:pos16 out_position16
        = < NCBI:SRA:pos16 > NCBI:SRA:make_position < 1 > ( out_2na_packed )
        | < NCBI:SRA:pos16 > NCBI:SRA:make_position < 1 > ( out_2cs_packed );
};


/*--------------------------------------------------------------------------
 * sra
 *  the NCBI SRA table
 */

/* history:
 *  1.0.1 - base explicitly upon sra #1.0.1
 *  1.0.2 - base explicitly upon sra #1.0.2, spotdesc_nocol #1.0.1
 *  1.0.3 - base explicitly upon sra #1.0.3, spotdesc_nocol #1.0.2
 */
table NCBI:SRA:tbl:sra_nopos #1.0.3 = INSDC:SRA:tbl:sra #1.0.3, NCBI:SRA:tbl:spotdesc_nocol #1.0.2
{
    // v1 declares the POSITION column for all tables
    // but leaves all physical columns unstated

    /* POSITION
     *  1-based coordinates
     *  describes a base's position on signal
     */
    column INSDC:position:one POSITION = out_position;
    readonly column NCBI:SRA:pos16 POSITION = out_position16;

    // zero-based coordinates available upon request
    readonly column INSDC:position:zero POSITION
        = ( INSDC:position:zero ) < I32 > diff < 1 > ( out_position );

    // statistics
    U64 base_count
        = < U64 > meta:value < "BASE_COUNT" > ();
    U64 spot_count
        = < U64 > meta:value < ".seq/spot" > ()
        | < U64 > meta:value < ".seq" > () ;


	/* INSDC:tbl:sequence inherited productions
	 *  cs_native
	 *  in_cs_key
	 *  out_cs_key
	 *  out_signal
	 *  in_dna_text
	 *  out_2cs_bin
	 *  out_2na_bin
	 *  out_4na_bin
	 *  out_dna_text
	 *  out_x2cs_bin
	 *  out_x2na_bin
	 *  in_color_text
	 *  out_2cs_packed
	 *  out_2na_packed
	 *  out_4na_packed
	 *  out_color_text
	 *  out_qual_phred
	 *  out_color_matrix
	 */

	/* INSDC:SRA:tbl:spotname inherited productions
	 *  out_x_coord
	 *  out_y_coord
	 *  out_name_fmt
	 *  out_spot_name
	 *  spot_ids_found
	 */

	/* INSDC:SRA:tbl:spotdesc inherited productions
	 *  trim_len
	 *  out_label
	 *  out_nreads
	 *  trim_start
	 *  out_read_len
	 *  out_label_len
	 *  out_rd_filter
	 *  out_read_type
	 *  out_read_start
	 *  out_label_start
	 *  static_fixed_spot_len
	 */

	/* INSDC:SRA:tbl:stats inherited productions
	 *  max_spot_id
	 *  min_spot_id
	 *  in_stats_bin
	 *  bio_base_count
	 */

	/* INSDC:SRA:tbl:sra inherited productions
	 *  out_platform
	 *  platform_name
	 */

	/* NCBI:SRA:tbl:spotdesc_nocol inherited productions
	 *  out_read_seg
	 *  out_label_seg
	 *  out_read_seg32
	 *  out_label_seg32
	 */

	/* NCBI:SRA:tbl:sra_nopos productions
	 *  out_position
	 *  out_position16
	 */
};

/* history:
 *  1.0.1 - base explicitly upon sra #1.0.1
 *  1.0.2 - base explicitly upon sra_nopos #1.0.2, pos #1.0.1
 *  1.0.3 - base explicitly upon sra_nopos #1.0.3
 */
table NCBI:SRA:tbl:sra #1.0.3 = NCBI:SRA:tbl:sra_nopos #1.0.3, NCBI:SRA:tbl:pos #1.0.1
{
    // the POSITION column is synthesized for all contemporary platforms but 454

	/* INSDC:tbl:sequence inherited productions
	 *  cs_native
	 *  in_cs_key
	 *  out_cs_key
	 *  out_signal
	 *  in_dna_text
	 *  out_2cs_bin
	 *  out_2na_bin
	 *  out_4na_bin
	 *  out_dna_text
	 *  out_x2cs_bin
	 *  out_x2na_bin
	 *  in_color_text
	 *  out_2cs_packed
	 *  out_2na_packed
	 *  out_4na_packed
	 *  out_color_text
	 *  out_qual_phred
	 *  out_color_matrix
	 */

	/* INSDC:SRA:tbl:spotname inherited productions
	 *  out_x_coord
	 *  out_y_coord
	 *  out_name_fmt
	 *  out_spot_name
	 *  spot_ids_found
	 */

	/* INSDC:SRA:tbl:spotdesc inherited productions
	 *  trim_len
	 *  out_label
	 *  out_nreads
	 *  trim_start
	 *  out_read_len
	 *  out_label_len
	 *  out_rd_filter
	 *  out_read_type
	 *  out_read_start
	 *  out_label_start
	 *  static_fixed_spot_len
	 */

	/* INSDC:SRA:tbl:stats inherited productions
	 *  max_spot_id
	 *  min_spot_id
	 *  in_stats_bin
	 *  bio_base_count
	 */

	/* INSDC:SRA:tbl:sra inherited productions
	 *  out_platform
	 *  platform_name
	 */

	/* NCBI:SRA:tbl:spotdesc_nocol inherited productions
	 *  out_read_seg
	 *  out_label_seg
	 *  out_read_seg32
	 *  out_label_seg32
	 */
};


/* v2 consolidates many of the auxiliary columns into a single treatment
 * left out are reads, qualities and platform-specific columns
 *
 * history:
 * 2.1.2 - base upon sra #1.0.3, spotdesc #1.0.2, stats #1.1.2
 */
table NCBI:SRA:tbl:sra_nopos #2.1.3 = INSDC:SRA:tbl:sra #1.0.3,
    NCBI:SRA:tbl:skeyname #3.0.1, NCBI:SRA:tbl:spotdesc #1.0.2, NCBI:SRA:tbl:stats #1.2.0
{
    // this is already specified in INSDC:SRA:tbl:sra #1
    // but putting it here will quiet down outputs
    INSDC:SRA:platform_id out_platform = .PLATFORM;

    column INSDC:position:one POSITION
        = out_position;
    readonly column NCBI:SRA:pos16 POSITION
        = cast ( _clip_position );
    INSDC:position:one _clip_position
        = < INSDC:position:one > clip < 0, 0xFFFF > ( out_position );
    readonly column INSDC:position:zero POSITION
        = ( INSDC:position:zero ) < I32 > diff < 1 > ( out_position );


	/* INSDC:tbl:sequence inherited productions
	 *  cs_native
	 *  in_cs_key
	 *  out_cs_key
	 *  out_signal
	 *  in_dna_text
	 *  out_2cs_bin
	 *  out_2na_bin
	 *  out_4na_bin
	 *  out_dna_text
	 *  out_x2cs_bin
	 *  out_x2na_bin
	 *  in_color_text
	 *  out_2cs_packed
	 *  out_2na_packed
	 *  out_4na_packed
	 *  out_color_text
	 *  out_qual_phred
	 *  out_color_matrix
	 */

	/* INSDC:SRA:tbl:spotdesc inherited productions
	 *  trim_len
	 *  trim_start
	 *  out_read_type
	 *  static_fixed_spot_len
	 */

	/* INSDC:SRA:tbl:stats inherited productions
	 *  in_stats_bin
	 */

	/* INSDC:SRA:tbl:sra inherited productions
	 *  out_platform
	 *  platform_name
	 */

	/* NCBI:SRA:tbl:skeyname inherited productions
	 *  in_spot_name_tok
	 */

	/* NCBI:SRA:tbl:spotdesc_nocol inherited productions
	 *  out_read_seg
	 *  out_label_seg
	 */

	/* NCBI:SRA:tbl:sra_nopos productions
	 *  out_position
	 */
};

/* most platforms don't have a native POSITION
 * mix in "pos" table to synthesize it
 *
 * history:
 *  2.1.2 - base upon sra#1.0.3, spotdesc #1.0.2, stats #1.1.2
 */
table NCBI:SRA:tbl:sra #2.1.3 = INSDC:SRA:tbl:sra #1.0.3,
    NCBI:SRA:tbl:skeyname #3.0.1, NCBI:SRA:tbl:spotdesc #1.0.2,
    NCBI:SRA:tbl:stats #1.2.0, NCBI:SRA:tbl:pos #1.0.1
{
    readonly column INSDC:position:one POSITION
        = out_position;
    readonly column NCBI:SRA:pos16 POSITION
        = out_position16;
    readonly column INSDC:position:zero POSITION
        = ( INSDC:position:zero ) < I32 > diff < 1 > ( out_position );


	/* INSDC:tbl:sequence inherited productions
	 *  cs_native
	 *  in_cs_key
	 *  out_cs_key
	 *  out_signal
	 *  in_dna_text
	 *  out_2cs_bin
	 *  out_2na_bin
	 *  out_4na_bin
	 *  out_dna_text
	 *  out_x2cs_bin
	 *  out_x2na_bin
	 *  in_color_text
	 *  out_2cs_packed
	 *  out_2na_packed
	 *  out_4na_packed
	 *  out_color_text
	 *  out_qual_phred
	 *  out_color_matrix
	 */

	/* INSDC:SRA:tbl:spotdesc inherited productions
	 *  trim_len
	 *  trim_start
	 *  out_read_type
	 *  static_fixed_spot_len
	 */

	/* INSDC:SRA:tbl:stats inherited productions
	 *  in_stats_bin
	 */

	/* INSDC:SRA:tbl:sra inherited productions
	 *  out_platform
	 *  platform_name
	 */

	/* NCBI:SRA:tbl:skeyname inherited productions
	 *  in_spot_name_tok
	 */
};
author	charles_s_test
date	Mon, 27 Nov 2017 11:21:07 -0500
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