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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/insdc/insdc.vschema @ 3:38ad1130d077 draft

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author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 /*===========================================================================
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2 *
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3 * PUBLIC DOMAIN NOTICE
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4 * National Center for Biotechnology Information
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5 *
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6 * This software/database is a "United States Government Work" under the
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7 * terms of the United States Copyright Act. It was written as part of
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8 * the author's official duties as a United States Government employee and
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9 * thus cannot be copyrighted. This software/database is freely available
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10 * to the public for use. The National Library of Medicine and the U.S.
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11 * Government have not placed any restriction on its use or reproduction.
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12 *
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13 * Although all reasonable efforts have been taken to ensure the accuracy
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14 * and reliability of the software and data, the NLM and the U.S.
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15 * Government do not and cannot warrant the performance or results that
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16 * may be obtained by using this software or data. The NLM and the U.S.
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17 * Government disclaim all warranties, express or implied, including
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18 * warranties of performance, merchantability or fitness for any particular
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19 * purpose.
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20 *
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21 * Please cite the author in any work or product based on this material.
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22 *
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23 * ===========================================================================
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24 *
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25 */
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26
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27 /*==========================================================================
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28 * INSDC types, constants
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29 */
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30 version 1;
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31
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32
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33 /*--------------------------------------------------------------------------
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34 * dna
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35 * represented in IUPAC characters
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36 */
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37 typedef ascii INSDC:dna:text;
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38
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39
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40 /*--------------------------------------------------------------------------
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41 * 4na
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42 * nucleotide data with all possible ambiguity
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43 * does not represent all possible EVENTS
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44 *
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45 * text encodings use the IUPAC character set
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46 * legal values: [ACMGRSVTWYHKDBNacmgrsvtwyhkdbn.]
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47 * canonical values: [ACMGRSVTWYHKDBN]
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48 *
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49 * binary values are 0..15 = { NACMGRSVTWYHKDBN }
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50 *
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51 * 4na values use bits for each letter:
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52 *
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53 * A | C | G | T
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54 * =================
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55 * N | | |
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56 * A * | | |
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57 * C | * | |
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58 * M * | * | |
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59 * G | | * |
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60 * R * | | * |
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61 * S | * | * |
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62 * V * | * | * |
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63 * T | | | *
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64 * W * | | | *
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65 * Y | * | | *
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66 * H * | * | | *
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67 * K | | * | *
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68 * D * | | * | *
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69 * B | * | * | *
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70 * N * | * | * | *
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71 */
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72 typedef U8 INSDC:4na:bin;
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73 typedef B1 INSDC:4na:packed [ 4 ];
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74
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75 const INSDC:4na:bin INSDC:4na:map:BINSET
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76 = [ 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15 ];
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77 const INSDC:dna:text INSDC:4na:map:CHARSET
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78 = ".ACMGRSVTWYHKDBN";
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79 const INSDC:dna:text INSDC:4na:accept:CHARSET
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80 = ".ACMGRSVTWYHKDBNacmgrsvtwyhkdbn";
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81
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82
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83 /*--------------------------------------------------------------------------
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84 * 2na - nucleotide data A,T,G,C
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85 * x2na - nucleotide data extended with single ambiguity value (N)
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86 *
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87 * text encodings use the IUPAC character set
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88 * legal values: [ACGTNacgtn.]
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89 * canonical values: [ACGTN]
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90 *
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91 * x2na values are 0..4 = { ACGTN }
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92 *
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93 * 2na values exclude N:
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94 * A = 0
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95 * C = 1
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96 * G = 2
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97 * T = 3
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98 */
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99 typedef U8 INSDC:2na:bin;
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100 typedef U8 INSDC:x2na:bin;
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101 typedef B1 INSDC:2na:packed [ 2 ];
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102
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103 const INSDC:2na:bin INSDC:2na:map:BINSET = [ 0,1,2,3 ];
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104 const INSDC:dna:text INSDC:2na:map:CHARSET = "ACGT";
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105 const INSDC:dna:text INSDC:2na:accept:CHARSET = "ACGTacgt";
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106 const INSDC:x2na:bin INSDC:x2na:map:BINSET = [ 0,1,2,3,4 ];
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107 const INSDC:dna:text INSDC:x2na:map:CHARSET = "ACGTN";
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108 const INSDC:dna:text INSDC:x2na:accept:CHARSET = "ACGTNacgtn.";
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109
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110
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111 /*--------------------------------------------------------------------------
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112 * color - color-space text
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113 * 2cs - color-space data 0,1,2,3
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114 * x2cs - color-space data extended with single ambiguity value (.)
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115 *
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116 * text encodings use the ASCII numeric character set
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117 * values: [0123.]
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118 *
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119 * x2cs values are 0..4 = { 0123. }
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120 *
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121 * 2cs values exclude '.':
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122 * '0' = 0
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123 * '1' = 1
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124 * '2' = 2
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125 * '3' = 3
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126 */
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127 typedef ascii INSDC:color:text;
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128 typedef U8 INSDC:2cs:bin;
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129 typedef U8 INSDC:x2cs:bin;
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130 typedef B1 INSDC:2cs:packed [ 2 ];
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131
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132 const INSDC:2cs:bin INSDC:2cs:map:BINSET = [ 0,1,2,3 ];
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133 const INSDC:color:text INSDC:2cs:map:CHARSET = "0123";
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134 const INSDC:color:text INSDC:2cs:accept:CHARSET = "0123";
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135 const INSDC:x2cs:bin INSDC:x2cs:map:BINSET = [ 0,1,2,3,4 ];
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136 const INSDC:color:text INSDC:x2cs:map:CHARSET = "0123.";
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137 const INSDC:color:text INSDC:x2cs:accept:CHARSET = "0123.";
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138
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139 const U8 INSDC:color:default_matrix =
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140 [
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141 0, 1, 2, 3, 4,
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142 1, 0, 3, 2, 4,
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143 2, 3, 0, 1, 4,
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144 3, 2, 1, 0, 4,
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145 4, 4, 4, 4, 4
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146 ];
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147
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148
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149 /*--------------------------------------------------------------------------
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150 * protein
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151 * represented in IUPAC characters
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152 */
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153 typedef ascii INSDC:protein:text;
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154
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155
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156 /*--------------------------------------------------------------------------
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157 * aa
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158 * protein data
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159 * text encodings use the IUPAC character set
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160 */
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161 typedef U8 INSDC:aa:bin;
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162
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163 const INSDC:aa:bin INSDC:aa:map:BINSET
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164 = [ 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 ];
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165 const INSDC:protein:text INSDC:aa:map:CHARSET
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166 = "ABCDEFGHIKLMNPQRSTVWXYZU*OJ";
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167 const INSDC:protein:text INSDC:aa:accept:CHARSET
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168 = "ABCDEFGHIJKLMNOPQRSTVWXYZU*abcdefghijklmnopqrstvwxyzu";
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169
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170
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171 /*--------------------------------------------------------------------------
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172 * quality
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173 * quality scoring values
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174 *
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175 * phred legal values: 0..63
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176 */
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177 typedef U8 INSDC:quality:phred;
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178 typedef I8 INSDC:quality:log_odds;
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179
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180 // text-encoding of quality scores
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181 // offsets are 33 = '!' and 64 = '@'
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182 typedef ascii INSDC:quality:text:phred_33;
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183 typedef ascii INSDC:quality:text:phred_64;
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184 typedef ascii INSDC:quality:text:log_odds_64;
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185
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186
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187 /*--------------------------------------------------------------------------
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188 * coordinate
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189 * zero and one based coordinates
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190 */
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191
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192 // 32 bit coordinates
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193 typedef I32 INSDC:coord:val;
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194 typedef U32 INSDC:coord:len;
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195
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196 // zero or one based coordinate system
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197 typedef INSDC:coord:val INSDC:coord:zero;
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198 typedef INSDC:coord:val INSDC:coord:one;
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199
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200 // POSITION types for relating bases to their location in signal
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201 typedef INSDC:coord:zero INSDC:position:zero;
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202 typedef INSDC:coord:one INSDC:position:one;
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203
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204 // one-based coordinate limits
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205 const INSDC:coord:one INSDC:coord:min:one = 0x80000001;
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206 const INSDC:coord:one INSDC:coord:max:one = 0x3FFFFFFF;
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207
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208 // zero-based coordinate limits
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209 const INSDC:coord:zero INSDC:coord:min:zero = 0x80000000;
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210 const INSDC:coord:zero INSDC:coord:max:zero = 0x3FFFFFFE;
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211
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212 /*-------------------------------------------------------------------------
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213 * read filters bits
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214 */
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215 typedef U8 INSDC:SRA:read_filter;
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216 const INSDC:SRA:read_filter SRA_READ_FILTER_PASS = 0;
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217 const INSDC:SRA:read_filter SRA_READ_FILTER_REJECT = 1;
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218 const INSDC:SRA:read_filter SRA_READ_FILTER_CRITERIA = 2;
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219 const INSDC:SRA:read_filter SRA_READ_FILTER_REDACTED = 3;
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220
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221 /*-------------------------------------------------------------------------
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222 * read type bits
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223 */
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224 typedef U8 INSDC:SRA:xread_type;
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225 const INSDC:SRA:xread_type SRA_READ_TYPE_TECHNICAL = 0;
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226 const INSDC:SRA:xread_type SRA_READ_TYPE_BIOLOGICAL = 1;
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227 const INSDC:SRA:xread_type SRA_READ_TYPE_FORWARD = 2;
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228 const INSDC:SRA:xread_type SRA_READ_TYPE_REVERSE = 4;
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229
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230 // original read-types included only technical and biological
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231 typedef INSDC:SRA:xread_type INSDC:SRA:read_type;
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232