/usr/lib/ncbi-vdb/insdc/insdc.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 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 | /*===========================================================================
*
* 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 types, constants
*/
version 1;
/*--------------------------------------------------------------------------
* dna
* represented in IUPAC characters
*/
typedef ascii INSDC:dna:text;
/*--------------------------------------------------------------------------
* 4na
* nucleotide data with all possible ambiguity
* does not represent all possible EVENTS
*
* text encodings use the IUPAC character set
* legal values: [ACMGRSVTWYHKDBNacmgrsvtwyhkdbn.]
* canonical values: [ACMGRSVTWYHKDBN]
*
* binary values are 0..15 = { NACMGRSVTWYHKDBN }
*
* 4na values use bits for each letter:
*
* A | C | G | T
* =================
* N | | |
* A * | | |
* C | * | |
* M * | * | |
* G | | * |
* R * | | * |
* S | * | * |
* V * | * | * |
* T | | | *
* W * | | | *
* Y | * | | *
* H * | * | | *
* K | | * | *
* D * | | * | *
* B | * | * | *
* N * | * | * | *
*/
typedef U8 INSDC:4na:bin;
typedef B1 INSDC:4na:packed [ 4 ];
const INSDC:4na:bin INSDC:4na:map:BINSET
= [ 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15 ];
const INSDC:dna:text INSDC:4na:map:CHARSET
= ".ACMGRSVTWYHKDBN";
const INSDC:dna:text INSDC:4na:accept:CHARSET
= ".ACMGRSVTWYHKDBNacmgrsvtwyhkdbn";
/*--------------------------------------------------------------------------
* 2na - nucleotide data A,T,G,C
* x2na - nucleotide data extended with single ambiguity value (N)
*
* text encodings use the IUPAC character set
* legal values: [ACGTNacgtn.]
* canonical values: [ACGTN]
*
* x2na values are 0..4 = { ACGTN }
*
* 2na values exclude N:
* A = 0
* C = 1
* G = 2
* T = 3
*/
typedef U8 INSDC:2na:bin;
typedef U8 INSDC:x2na:bin;
typedef B1 INSDC:2na:packed [ 2 ];
const INSDC:2na:bin INSDC:2na:map:BINSET = [ 0,1,2,3 ];
const INSDC:dna:text INSDC:2na:map:CHARSET = "ACGT";
const INSDC:dna:text INSDC:2na:accept:CHARSET = "ACGTacgt";
const INSDC:x2na:bin INSDC:x2na:map:BINSET = [ 0,1,2,3,4 ];
const INSDC:dna:text INSDC:x2na:map:CHARSET = "ACGTN";
const INSDC:dna:text INSDC:x2na:accept:CHARSET = "ACGTNacgtn.";
/*--------------------------------------------------------------------------
* color - color-space text
* 2cs - color-space data 0,1,2,3
* x2cs - color-space data extended with single ambiguity value (.)
*
* text encodings use the ASCII numeric character set
* values: [0123.]
*
* x2cs values are 0..4 = { 0123. }
*
* 2cs values exclude '.':
* '0' = 0
* '1' = 1
* '2' = 2
* '3' = 3
*/
typedef ascii INSDC:color:text;
typedef U8 INSDC:2cs:bin;
typedef U8 INSDC:x2cs:bin;
typedef B1 INSDC:2cs:packed [ 2 ];
const INSDC:2cs:bin INSDC:2cs:map:BINSET = [ 0,1,2,3 ];
const INSDC:color:text INSDC:2cs:map:CHARSET = "0123";
const INSDC:color:text INSDC:2cs:accept:CHARSET = "0123";
const INSDC:x2cs:bin INSDC:x2cs:map:BINSET = [ 0,1,2,3,4 ];
const INSDC:color:text INSDC:x2cs:map:CHARSET = "0123.";
const INSDC:color:text INSDC:x2cs:accept:CHARSET = "0123.";
const U8 INSDC:color:default_matrix =
[
0, 1, 2, 3, 4,
1, 0, 3, 2, 4,
2, 3, 0, 1, 4,
3, 2, 1, 0, 4,
4, 4, 4, 4, 4
];
/*--------------------------------------------------------------------------
* protein
* represented in IUPAC characters
*/
typedef ascii INSDC:protein:text;
/*--------------------------------------------------------------------------
* aa
* protein data
* text encodings use the IUPAC character set
*/
typedef U8 INSDC:aa:bin;
const INSDC:aa:bin INSDC:aa:map:BINSET
= [ 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 ];
const INSDC:protein:text INSDC:aa:map:CHARSET
= "ABCDEFGHIKLMNPQRSTVWXYZU*OJ";
const INSDC:protein:text INSDC:aa:accept:CHARSET
= "ABCDEFGHIJKLMNOPQRSTVWXYZU*abcdefghijklmnopqrstvwxyzu";
/*--------------------------------------------------------------------------
* quality
* quality scoring values
*
* phred legal values: 0..63
*/
typedef U8 INSDC:quality:phred;
typedef I8 INSDC:quality:log_odds;
// text-encoding of quality scores
// offsets are 33 = '!' and 64 = '@'
typedef ascii INSDC:quality:text:phred_33;
typedef ascii INSDC:quality:text:phred_64;
typedef ascii INSDC:quality:text:log_odds_64;
/*--------------------------------------------------------------------------
* coordinate
* zero and one based coordinates
*/
// 32 bit coordinates
typedef I32 INSDC:coord:val;
typedef U32 INSDC:coord:len;
// zero or one based coordinate system
typedef INSDC:coord:val INSDC:coord:zero;
typedef INSDC:coord:val INSDC:coord:one;
// POSITION types for relating bases to their location in signal
typedef INSDC:coord:zero INSDC:position:zero;
typedef INSDC:coord:one INSDC:position:one;
// one-based coordinate limits
const INSDC:coord:one INSDC:coord:min:one = 0x80000001;
const INSDC:coord:one INSDC:coord:max:one = 0x3FFFFFFF;
// zero-based coordinate limits
const INSDC:coord:zero INSDC:coord:min:zero = 0x80000000;
const INSDC:coord:zero INSDC:coord:max:zero = 0x3FFFFFFE;
/*-------------------------------------------------------------------------
* read filters bits
*/
typedef U8 INSDC:SRA:read_filter;
const INSDC:SRA:read_filter SRA_READ_FILTER_PASS = 0;
const INSDC:SRA:read_filter SRA_READ_FILTER_REJECT = 1;
const INSDC:SRA:read_filter SRA_READ_FILTER_CRITERIA = 2;
const INSDC:SRA:read_filter SRA_READ_FILTER_REDACTED = 3;
/*-------------------------------------------------------------------------
* read type bits
*/
typedef U8 INSDC:SRA:xread_type;
const INSDC:SRA:xread_type SRA_READ_TYPE_TECHNICAL = 0;
const INSDC:SRA:xread_type SRA_READ_TYPE_BIOLOGICAL = 1;
const INSDC:SRA:xread_type SRA_READ_TYPE_FORWARD = 2;
const INSDC:SRA:xread_type SRA_READ_TYPE_REVERSE = 4;
// original read-types included only technical and biological
typedef INSDC:SRA:xread_type INSDC:SRA:read_type;
|