/usr/lib/ncbi-vdb/sra/helicos.vschema is in libncbi-vdb2 2.8.2-2+dfsg-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 | /*===========================================================================
*
* 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 Helicos Sequence Read Archive schema
*/
version 1;
include '/usr/lib/ncbi-vdb/ncbi/sra.vschema';
include '/usr/lib/ncbi-vdb/ncbi/spotname.vschema';
/*--------------------------------------------------------------------------
* functions
*/
/* tokenize_spot_name
* scans name on input
* tokenizes into parts
*/
extern function NCBI:SRA:spot_name_token
NCBI:SRA:Helicos:tokenize_spot_name #1 ( ascii name );
/* Helicos:tbl
*
* history:
* 1.0.1 - explictly base upon ancestry
* 1.0.2 - base explicitly upon latest ancestry
* 1.0.3 - base explicitly upon latest ancestry
* 1.0.4 - base explicitly upon latest ancestry
*/
table NCBI:SRA:Helicos:tbl:v2 #1.0.4
= NCBI:SRA:tbl:sra #2.1.3
, NCBI:tbl:base_space #2.0.3
, NCBI:tbl:phred_quality #2.0.3
{
ascii platform_name
= < ascii > echo < "HELICOS" > ();
/* NAME tokenizing and coordinates
* most work happens in skeyname table
* we still obtain REGION from name
*/
readonly column INSDC:coord:val CHANNEL = ( INSDC:coord:val )
NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:L > ( _out_name, out_spot_name_tok );
readonly column INSDC:coord:val FIELD = ( 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:Helicos:tokenize_spot_name ( _out_name );
readonly column INSDC:coord:val CAMERA = out_x_coord;
readonly column INSDC:coord:val POS = out_y_coord;
NCBI:SRA:spot_name_token in_spot_name_tok
= NCBI:SRA:Helicos:tokenize_spot_name ( NAME );
INSDC:coord:zero trim_start
= < INSDC:coord:zero > echo < 0 > ();
INSDC:coord:len trim_len = spot_len;
};
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