/usr/lib/ncbi/schema/ion-torrent.vschema is in sra-toolkit 2.1.7a-1ubuntu2.
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 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 | /*===========================================================================
*
* 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 Ion Torrent Sequence Read Archive schema
*/
version 1;
include 'ncbi/sra.vschema';
include 'ncbi/spotname.vschema';
include 'ncbi/clip.vschema';
/*--------------------------------------------------------------------------
* functions
*/
/* tokenize_spot_name
* scans name on input
* tokenizes into parts
*/
extern function NCBI:SRA:spot_name_token
NCBI:SRA:IonTorrent:tokenize_spot_name #1 ( ascii name );
/*--------------------------------------------------------------------------
* table
*/
physical INSDC:position:one NCBI:SRA:IonTorrent:encoding:POSITION #1
{
decode
{
I32 pos_1st_deriv = iunzip ( @ );
return ( INSDC:position:one ) < I32 > integral ( pos_1st_deriv );
}
encode
{
I32 pos_1st_deriv = < I32 > deriv ( @ );
return izip ( pos_1st_deriv );
}
}
/* IonTorrent:tbl
*
* history:
* 1.0.1 - updated ancestry
* 1.0.2 - updated ancestry
* 1.0.3 - updated ancestry
*/
table NCBI:SRA:IonTorrent:tbl:v2 #1.0.3
= INSDC:SRA:tbl:sra #1.0.3
, NCBI:SRA:tbl:sra_nopos #2.1.3
, NCBI:tbl:base_space #2.0.3
, NCBI:tbl:phred_quality #2.0.3
, NCBI:SRA:tbl:clip #1.0.2
{
/* PLATFORM is always ION_TORRENT */
ascii platform_name
= < ascii > echo < "ION_TORRENT" > ();
/* NAME tokenizing and coordinates
* most work happens in skeyname table
*/
NCBI:SRA:spot_name_token out_spot_name_tok
= NCBI:SRA:IonTorrent:tokenize_spot_name ( _out_name );
NCBI:SRA:spot_name_token in_spot_name_tok
= NCBI:SRA:IonTorrent:tokenize_spot_name ( NAME );
// special sequences
column < INSDC:dna:text > zip_encoding FLOW_CHARS;
column < INSDC:dna:text > zip_encoding KEY_SEQUENCE;
// position stored as normal 1-based coordinate
INSDC:position:one out_position = .POSITION;
physical column NCBI:SRA:IonTorrent:encoding:POSITION
.POSITION = POSITION;
// 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;
// signal
column < NCBI:isamp1 > izip_encoding SIGNAL;
};
|