/usr/lib/ncbi-vdb/sra/generic-fastq.vschema is in libncbi-vdb2 2.8.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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 Generic Fastq Sequence Read Archive schema
*/
version 1;
include '/usr/lib/ncbi-vdb/insdc/sra.vschema';
include '/usr/lib/ncbi-vdb/ncbi/sra.vschema';
include '/usr/lib/ncbi-vdb/ncbi/clip.vschema';
include '/usr/lib/ncbi-vdb/ncbi/spotname.vschema';
/* tokenize_spot_name - currently ascii only capability */
extern function NCBI:SRA:spot_name_token
NCBI:SRA:GenericFastq:tokenize_spot_name #1 ( ascii name );
/*--------------------------------------------------------------------------
* NCBI:SRA:GenericFastq:sequence
* Generic Fastq SRA Platform
*/
table NCBI:SRA:GenericFastq:sequence #1
= NCBI:SRA:tbl:sra #2.1.3
, NCBI:tbl:base_space #2.0.3
, NCBI:tbl:phred_quality #2.0.4
, NCBI:SRA:tbl:clip #1.0.2
{
ascii platform_name
= < ascii > echo < "UNDEFINED" > ();
INSDC:SRA:platform_id out_platform
= < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
/* ascii only spot name tokenizer */
NCBI:SRA:spot_name_token out_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
NCBI:SRA:spot_name_token in_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
/* clips */
physical column < INSDC:coord:one > izip_encoding
.CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
}
database NCBI:SRA:GenericFastq:db #1
{
table NCBI:SRA:GenericFastq:sequence #1.0 SEQUENCE;
};
/*--------------------------------------------------------------------------
* NCBI:SRA:GenericFastq:sequence_no_name
* Generic Fastq SRA Platform (without name)
*/
table NCBI:SRA:GenericFastq:sequence_no_name #1
= NCBI:SRA:tbl:sra #2.1.3
, NCBI:tbl:base_space #2.0.3
, NCBI:tbl:phred_quality #2.0.4
, NCBI:SRA:tbl:clip #1.0.2
{
ascii platform_name
= < ascii > echo < "UNDEFINED" > ();
INSDC:SRA:platform_id out_platform
= < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
/* clips */
physical column < INSDC:coord:one > izip_encoding
.CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
}
database NCBI:SRA:GenericFastqNoNames:db #1
{
table NCBI:SRA:GenericFastq:sequence_no_name #1.0 SEQUENCE;
};
/*--------------------------------------------------------------------------
* NCBI:SRA:GenericFastq:sequence_log_odds
* Generic Fastq SRA Platform (for log_odds)
*/
table NCBI:SRA:GenericFastq:sequence_log_odds #1
= NCBI:SRA:tbl:sra #2.1.3
, NCBI:tbl:base_space #2.0.3
, NCBI:tbl:log_odds_quality #2.1.0
, NCBI:SRA:tbl:clip #1.0.2
{
ascii platform_name
= < ascii > echo < "UNDEFINED" > ();
INSDC:SRA:platform_id out_platform
= < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
/* ascii only spot name tokenizer */
NCBI:SRA:spot_name_token out_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
NCBI:SRA:spot_name_token in_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
/* clips */
physical column < INSDC:coord:one > izip_encoding
.CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
}
database NCBI:SRA:GenericFastqLogOdds:db #1
{
table NCBI:SRA:GenericFastq:sequence_log_odds #1.0 SEQUENCE;
};
/*--------------------------------------------------------------------------
* NCBI:SRA:GenericFastq:sequence_nanopore
* Oxford Nanopore SRA Platform
*/
table NCBI:SRA:GenericFastq:sequence_nanopore #1
= NCBI:SRA:tbl:sra #2.1.3
, NCBI:tbl:base_space #2.0.3
, NCBI:tbl:phred_quality #2.0.4
{
ascii platform_name
= < ascii > echo < "OXFORD_NANOPORE" > ();
INSDC:SRA:platform_id out_platform
= < INSDC:SRA:platform_id > echo < SRA_PLATFORM_OXFORD_NANOPORE > ();
/* ascii only spot name tokenizer */
NCBI:SRA:spot_name_token out_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
NCBI:SRA:spot_name_token in_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
/* channel and read number columns */
extern column < U32 > izip_encoding #1 CHANNEL;
extern column < U32 > izip_encoding #1 READ_NUMBER;
}
/*--------------------------------------------------------------------------
* NCBI:SRA:GenericFastq:consensus_nanopore
* Oxford Nanopore SRA Platform
*/
table NCBI:SRA:GenericFastq:consensus_nanopore #1
= NCBI:SRA:tbl:sra #2.1.3
, NCBI:tbl:base_space #2.0.3
, NCBI:tbl:phred_quality #2.0.4
{
ascii platform_name
= < ascii > echo < "OXFORD_NANOPORE" > ();
INSDC:SRA:platform_id out_platform
= < INSDC:SRA:platform_id > echo < SRA_PLATFORM_OXFORD_NANOPORE > ();
/* ascii only spot name tokenizer */
NCBI:SRA:spot_name_token out_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
NCBI:SRA:spot_name_token in_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
/* channel and read number columns */
extern column < U32 > izip_encoding #1 CHANNEL;
extern column < U32 > izip_encoding #1 READ_NUMBER;
}
database NCBI:SRA:GenericFastqNanopore:db #1
{
table NCBI:SRA:GenericFastq:sequence_nanopore #1.0 SEQUENCE;
table NCBI:SRA:GenericFastq:consensus_nanopore #1.0 CONSENSUS;
};
database NCBI:SRA:GenericFastqNanoporeConsensusOnly:db #1
{
table NCBI:SRA:GenericFastq:consensus_nanopore #1.0 CONSENSUS;
};
/*--------------------------------------------------------------------------
* NCBI:SRA:GenericFastq:absolid
* Generic fastq for AB Solid platform
*/
table NCBI:SRA:GenericFastq:absolid #1
= NCBI:SRA:tbl:sra #2.1.3
, NCBI:tbl:color_space #2.1.0
, NCBI:tbl:phred_quality #2.0.4
, NCBI:SRA:tbl:clip #1.0.2
{
ascii platform_name
= < ascii > echo < "UNDEFINED" > ();
INSDC:SRA:platform_id out_platform
= < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
/* ascii only spot name tokenizer */
NCBI:SRA:spot_name_token out_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
NCBI:SRA:spot_name_token in_spot_name_tok
= NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
/* clips */
physical column < INSDC:coord:one > izip_encoding
.CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
physical column < INSDC:coord:one > izip_encoding
.CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
}
database NCBI:SRA:GenericFastqAbsolid:db #1
{
table NCBI:SRA:GenericFastq:absolid #1.0 SEQUENCE;
};
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