/usr/lib/ncbi/schema/sra.vschema is in sra-toolkit 2.1.7a-1ubuntu2.
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*
* 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 );
/* 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
*/
};
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