/*===========================================================================
*
* 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.
*
* ===========================================================================
*
*/
/*==========================================================================
* INSDC Sequence Read Archive schema
*/
version 1;
include 'insdc/seq.vschema';
/*--------------------------------------------------------------------------
* types
*/
/* spotid_t
* unique id given to every spot
*/
typedef U32 INSDC:SRA:spotid_t;
/* spot_ids_found
*/
typedef U64 INSDC:SRA:spot_ids_found [ 4 ];
/*--------------------------------------------------------------------------
* functions
*/
/* format_spot_name
* given a name format string, X, and Y
* produce a reconstructed spot name string
*
* "name_fmt" [ DATA ] - name format string ( see format explanation below )
*
* "X" [ DATA ] - X coordinate for spot
*
* "Y" [ DATA ] - Y coordinate for spot
*
* "spot_name" [ DATA, OPTIONAL ] - potential source of unformatted names
*
* SYNOPSIS:
* "name_fmt" may have any ASCII characters
* the special character '$' is an escape symbol
* when followed by a recognized format character,
* both the '$' and its format character will be
* replaced with a numeral generated from X and/or Y.
*
* when "spot_name" is present and the "name_fmt" row is empty,
* output is taken verbatim from "spot_name"
*/
function
ascii INSDC:SRA:format_spot_name #1 ( ascii name_fmt , I32 X , I32 Y * ascii spot_name );
function
ascii INSDC:SRA:format_spot_name_no_coord #1 ( ascii name_fmt * ascii spot_name );
/* spot2read_filter
* takes input from whole-spot filter bits
* produces older-style array of per-read filter bits
* based upon dimension and possibly type of "out_read_type"
*/
function INSDC:SRA:read_filter
INSDC:SRA:spot2read_filter #1 ( INSDC:SRA:spot_filter out_spot_filter, INSDC:SRA:xread_type out_read_type );
/* read2spot_filter
* takes input older-style array of per-read filter bits
* produces whole-spot filter bits
*
* Rules are: (listed in order of precedence)
* 1) REJECT, if any reads are REJECT
* 2) REDACTED, '' REDACTED
* 3) CRITERIA, '' CRITERIA
* 4) else PASS
*
*/
function INSDC:SRA:spot_filter
INSDC:SRA:read2spot_filter #1 ( INSDC:SRA:read_filter out_read_filter );
/*--------------------------------------------------------------------------
* spotcoord
* spot coordinate table
* gives X and Y and potentially other common coordinates
*/
table INSDC:SRA:tbl:spotcoord #1
{
/* X, Y
* 32 ( or 16 ) bit coordinates within plate region
* the coordinate system ( zero or one-based ) is unspecified
*/
extern default column INSDC:coord:val X = out_x_coord;
extern default column INSDC:coord:val Y = out_y_coord;
// backward compatibility for 16-bit unsigned coordinates
extern readonly column U16 X = cast ( x_clip_U16 );
extern readonly column U16 Y = cast ( y_clip_U16 );
// clip signed 32-bit coordinates to unsigned 16-bit
INSDC:coord:val x_clip_U16
= < INSDC:coord:val > clip < 0, 0xFFFF > ( out_x_coord );
INSDC:coord:val y_clip_U16
= < INSDC:coord:val > clip < 0, 0xFFFF > ( out_y_coord );
/* INSDC:SRA:tbl:spotcoord virtual productions
* out_x_coord
* out_y_coord
*/
};
/*--------------------------------------------------------------------------
* spotname
* spot name table
* the name column is normally indexed
*
* history:
* 1.0.1 - split X and Y into spotcoord table
* 1.1.0 - added ability to get name from TRACE_NAME
*/
table INSDC:SRA:tbl:spotname #1.1 = INSDC:SRA:tbl:spotcoord #1
{
/* NAME
* external name for spot
*/
extern column ascii NAME = _out_name;
/* SPOT_IDS_FOUND
* lookup by NAME column
*/
readonly column INSDC:SRA:spot_ids_found SPOT_IDS_FOUND
= spot_ids_found;
/* default rules */
// assemble NAME column output in order of preference
ascii _out_name
= INSDC:SRA:format_spot_name ( out_name_fmt, out_x_coord, out_y_coord, out_spot_name )
| INSDC:SRA:format_spot_name ( out_name_fmt, out_x_coord, out_y_coord )
| INSDC:SRA:format_spot_name_no_coord (out_name_fmt)
| out_spot_name
| out_trace_name
;
/* INSDC:SRA:tbl:spotcoord inherited virtual productions
* out_x_coord
* out_y_coord
*/
/* INSDC:SRA:tbl:spotname virtual productions
* out_name_fmt
* out_spot_name
* spot_ids_found
*/
};
/*--------------------------------------------------------------------------
* spotdesc
* spot descriptor table
*
* history:
* 1.0.1 - base explicitly upon sequence #1.0.1
* 1.0.2 - added alternate taps for in_read_type and in_read_len
* 1.1.0 - added SPOT_FILTER
*/
table INSDC:SRA:tbl:spotdesc #1.0.2 = INSDC:tbl:sequence #1.0.1
{
/* NREADS
* describes the number of reads within spot
*/
extern column U8 NREADS = out_nreads;
/* SPOT_LEN
* length of sequence
* FIXED_SPOT_LEN
* non-zero if sequence length is fixed throughout table
*/
readonly column INSDC:coord:len SPOT_LEN = spot_len;
readonly column INSDC:coord:len FIXED_SPOT_LEN = fixed_spot_len;
/* TRIM_START
* TRIM_LEN
* define the spot segment after applying trimming
* trimming may be based upon technical segments and read quality
*/
readonly column INSDC:coord:zero TRIM_START
= trim_start
| < INSDC:coord:zero> echo < 0 > ();
readonly column INSDC:coord:one TRIM_START
= ( INSDC:coord:one ) < I32 > sum < 1 > ( trim_start )
| < INSDC:coord:one> echo < 1 > ();
readonly column INSDC:coord:len TRIM_LEN
= trim_len
| spot_len;
/* LABEL
* LABEL_START, LABEL_LEN
* column pair for writing read labels
* the label text for all reads is concatenated to form the LABEL row
* starting coordinates and lengths delineate labels by read
*
* NB - row length for LABEL_START/LEN === NREADS,
* row length for LABEL === SUM ( LABEL_LEN [ n ] ) for NREADS
*/
extern column ascii LABEL = out_label;
extern column INSDC:coord:zero LABEL_START = out_label_start;
extern column INSDC:coord:len LABEL_LEN = out_label_len;
// 16-bit versions
readonly column U16 LABEL_START = cast ( out_label_start );
readonly column U16 LABEL_LEN = cast ( out_label_len );
/* READ_TYPE
* binary values giving type of a read
*
* NB - row length === NREADS
*/
extern default column INSDC:SRA:xread_type READ_TYPE = out_read_type;
INSDC:SRA:xread_type in_read_type
= READ_TYPE
| _alt_in_read_type;
readonly column INSDC:SRA:read_type READ_TYPE
= out_read_type
| < INSDC:SRA:xread_type, INSDC:SRA:read_type > map < [ 0,1,2,3,4,5,6,7 ], [ 0,1,0,1,0,1,0,1 ] > ( out_read_type );
/* READ_START
* READ_LEN
* define starting coordinates and length of read segments
*
* NB - row length === NREADS
*/
extern default column INSDC:coord:zero READ_START
= out_read_start;
extern column INSDC:coord:one READ_START
= ( INSDC:coord:one ) < I32 > sum < 1 > ( out_read_start );
extern column INSDC:coord:len READ_LEN = out_read_len;
// 16-bit versions
readonly column U16 READ_START = cast ( out_read_start );
readonly column U16 READ_LEN = cast ( out_read_len );
INSDC:coord:zero in_read_start
= READ_START
;
INSDC:coord:len in_read_len
= READ_LEN
| _alt_in_read_len;
/* READ_FILTER
* bits indicate usability of sequence
* always available
*/
extern column INSDC:SRA:read_filter READ_FILTER
= out_rd_filter
| INSDC:SRA:spot2read_filter ( out_spot_filter, out_read_type )
| < INSDC:SRA:read_filter > echo < SRA_READ_FILTER_PASS > ( out_read_type )
;
// only available if READ_FILTER is being written
INSDC:SRA:read_filter in_read_filter
= READ_FILTER
;
// RD_FILTER - only available if physical column is present
extern readonly column INSDC:SRA:read_filter RD_FILTER
= out_rd_filter
;
/* SPOT_FILTER
* like READ_FILTER, but applies to entire spot
*/
INSDC:SRA:spot_filter in_spot_filter_0
= SPOT_FILTER
| INSDC:SRA:read2spot_filter ( in_read_filter )
| < INSDC:SRA:spot_filter > echo < SRA_SPOT_FILTER_PASS > ()
;
extern column INSDC:SRA:spot_filter SPOT_FILTER
= out_spot_filter
| INSDC:SRA:read2spot_filter ( out_rd_filter )
| < INSDC:SRA:spot_filter > echo < SRA_SPOT_FILTER_PASS > ()
;
/* spot_len is used internally */
INSDC:coord:len spot_len
= base_space_spot_len
| color_space_spot_len
| align_spot_len;
INSDC:coord:len fixed_spot_len
= static_fixed_spot_len
| base_space_fixed_spot_len
| color_space_fixed_spot_len;
/* INSDC:tbl:sequence inherited virtual productions
* out_2cs_packed
* out_2na_packed
*/
/* INSDC:SRA:tbl:spotdesc 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
*/
};
/*--------------------------------------------------------------------------
* stats
* run and spot-group statistics
*
* history:
* 1.1.0 - added CMP_BASE_COUNT
*/
table INSDC:SRA:tbl:stats #1.1
{
readonly column INSDC:SRA:spotid_t MIN_SPOT_ID
= min_spot_id
| < INSDC:SRA:spotid_t > echo < 1 > ();
readonly column INSDC:SRA:spotid_t MAX_SPOT_ID
= max_spot_id
| cast ( spot_count );
readonly column U64
SPOT_COUNT = spot_count;
readonly column U64
BASE_COUNT = base_count;
readonly column U64
BIO_BASE_COUNT = bio_base_count;
readonly column U64 CMP_BASE_COUNT
= cmp_base_count
| base_count;
U8 stats_dummy = in_stats_bin;
/* INSDC:SRA:tbl:stats productions
* base_count
* spot_count
* max_spot_id
* min_spot_id
* in_stats_bin
* bio_base_count
* cmp_base_count
*/
};
/*--------------------------------------------------------------------------
* sra
* the INSDC SRA table
*
* history:
* 1.0.1 - base explicitly upon spotname #1.0.1
* 1.0.2 - base explicitly upon sequence #1.0.1, spotdesc #1.0.1
* 1.0.3 - base upon spotdesc #1.0.2
* 1.0.4 - base upon spotname #1.1
*/
// platform constants from <insdc/sra.h>
typedef U8 INSDC:SRA:platform_id;
const INSDC:SRA:platform_id SRA_PLATFORM_UNDEFINED = 0;
const INSDC:SRA:platform_id SRA_PLATFORM_454 = 1;
const INSDC:SRA:platform_id SRA_PLATFORM_ILLUMINA = 2;
const INSDC:SRA:platform_id SRA_PLATFORM_ABSOLID = 3;
const INSDC:SRA:platform_id SRA_PLATFORM_COMPLETE_GENOMICS = 4;
const INSDC:SRA:platform_id SRA_PLATFORM_HELICOS = 5;
const INSDC:SRA:platform_id SRA_PLATFORM_PACBIO_SMRT = 6;
const INSDC:SRA:platform_id SRA_PLATFORM_ION_TORRENT = 7;
const INSDC:SRA:platform_id SRA_PLATFORM_CAPILLARY = 8;
const INSDC:SRA:platform_id SRA_PLATFORM_OXFORD_NANOPORE = 9;
table INSDC:SRA:tbl:sra #1.0.4 =
INSDC:tbl:sequence #1.0.1,
INSDC:SRA:tbl:spotname #1.1,
INSDC:SRA:tbl:spotdesc #1.0.2,
INSDC:SRA:tbl:stats #1.1.0
{
/* PLATFORM
* platform description
* one version returns a constant defined above
* while the other returns a textual representation
*/
extern column INSDC:SRA:platform_id PLATFORM
= .PLATFORM
| out_platform
;
readonly column ascii PLATFORM
= platform_name
;
physical column < INSDC:SRA:platform_id > zip_encoding .PLATFORM
= PLATFORM
;
/* SPOT_ID
* reports spot id of current row
*/
extern column INSDC:SRA:spotid_t SPOT_ID
= < INSDC:SRA:spotid_t > add_row_id ( .SPOT_ID )
| cast ( rowid_64 )
;
I64 rowid_64 = row_id ();
physical column < INSDC:SRA:spotid_t > izip_encoding .SPOT_ID
= < INSDC:SRA:spotid_t > sub_row_id ( SPOT_ID )
;
/* SPOT_GROUP
* a name denoting group membership, ''
* used for "barcode" support
*/
extern column ascii SPOT_GROUP
= out_spot_group
| .SPOT_GROUP
| < ascii > echo < '' > ()
;
ascii in_spot_group = SPOT_GROUP;
physical column
< ascii > zip_encoding < Z_DEFAULT_STRATEGY, Z_BEST_SPEED > .SPOT_GROUP
= in_spot_group
;
/* INSDC:tbl:sequence inherited virtual 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:spotcoord inherited virtual productions
* out_x_coord
* out_y_coord
*/
/* INSDC:SRA:tbl:spotname inherited virtual productions
* 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
* base_count
* spot_count
* max_spot_id
* min_spot_id
* in_stats_bin
* bio_base_count
*/
/* INSDC:SRA:tbl:sra productions
* out_platform
* platform_name
*/
};