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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/insdc/sra.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 Sequence Read Archive schema
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29 */
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30 version 1;
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31
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32 include 'insdc/seq.vschema';
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33
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34
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35 /*--------------------------------------------------------------------------
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36 * types
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37 */
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38
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39 /* spotid_t
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40 * unique id given to every spot
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41 */
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42 typedef U32 INSDC:SRA:spotid_t;
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43
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44
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45 /* spot_ids_found
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46 */
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47 typedef U64 INSDC:SRA:spot_ids_found [ 4 ];
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48
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49
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50 /*--------------------------------------------------------------------------
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51 * functions
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52 */
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53
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54
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55 /* format_spot_name
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56 * given a name format string, X, and Y
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57 * produce a reconstructed spot name string
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58 *
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59 * "name_fmt" [ DATA ] - name format string ( see format explanation below )
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60 *
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61 * "X" [ DATA ] - X coordinate for spot
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62 *
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63 * "Y" [ DATA ] - Y coordinate for spot
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64 *
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65 * "spot_name" [ DATA, OPTIONAL ] - potential source of unformatted names
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66 *
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67 * SYNOPSIS:
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68 * "name_fmt" may have any ASCII characters
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69 * the special character '$' is an escape symbol
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70 * when followed by a recognized format character,
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71 * both the '$' and its format character will be
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72 * replaced with a numeral generated from X and/or Y.
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73 *
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74 * when "spot_name" is present and the "name_fmt" row is empty,
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75 * output is taken verbatim from "spot_name"
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76 */
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77 function
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78 ascii INSDC:SRA:format_spot_name #1 ( ascii name_fmt , I32 X , I32 Y * ascii spot_name );
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79
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80 function
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81 ascii INSDC:SRA:format_spot_name_no_coord #1 ( ascii name_fmt * ascii spot_name );
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82
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83
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84 /*--------------------------------------------------------------------------
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85 * spotcoord
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86 * spot coordinate table
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87 * gives X and Y and potentially other common coordinates
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88 */
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89 table INSDC:SRA:tbl:spotcoord #1
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90 {
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91 /* X, Y
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92 * 32 ( or 16 ) bit coordinates within plate region
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93 * the coordinate system ( zero or one-based ) is unspecified
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94 */
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95 extern default column INSDC:coord:val X = out_x_coord;
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96 extern default column INSDC:coord:val Y = out_y_coord;
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97
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98 // backward compatibility for 16-bit unsigned coordinates
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99 extern readonly column U16 X = cast ( x_clip_U16 );
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100 extern readonly column U16 Y = cast ( y_clip_U16 );
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101
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102 // clip signed 32-bit coordinates to unsigned 16-bit
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103 INSDC:coord:val x_clip_U16
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104 = < INSDC:coord:val > clip < 0, 0xFFFF > ( out_x_coord );
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105 INSDC:coord:val y_clip_U16
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106 = < INSDC:coord:val > clip < 0, 0xFFFF > ( out_y_coord );
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107
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108
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109 /* INSDC:SRA:tbl:spotcoord virtual productions
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110 * out_x_coord
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111 * out_y_coord
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112 */
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113 };
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114
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115
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116 /*--------------------------------------------------------------------------
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117 * spotname
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118 * spot name table
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119 * the name column is normally indexed
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120 *
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121 * history:
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122 * 1.0.1 - split X and Y into spotcoord table
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123 */
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124 table INSDC:SRA:tbl:spotname #1.0.1 = INSDC:SRA:tbl:spotcoord #1
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125 {
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126 /* NAME
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127 * external name for spot
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128 */
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129 extern column ascii NAME = _out_name;
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130
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131
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132 /* SPOT_IDS_FOUND
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133 * lookup by NAME column
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134 */
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135 readonly column INSDC:SRA:spot_ids_found SPOT_IDS_FOUND
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136 = spot_ids_found;
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137
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138
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139 /* default rules */
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140
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141 // assemble NAME column output in order of preference
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142 ascii _out_name
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143 = INSDC:SRA:format_spot_name ( out_name_fmt, out_x_coord, out_y_coord, out_spot_name )
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144 | INSDC:SRA:format_spot_name ( out_name_fmt, out_x_coord, out_y_coord )
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145 | INSDC:SRA:format_spot_name_no_coord (out_name_fmt)
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146 | out_spot_name;
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147
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148
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149 /* INSDC:SRA:tbl:spotcoord inherited virtual productions
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150 * out_x_coord
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151 * out_y_coord
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152 */
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153
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154 /* INSDC:SRA:tbl:spotname virtual productions
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155 * out_name_fmt
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156 * out_spot_name
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157 * spot_ids_found
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158 */
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159 };
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160
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161
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162 /*--------------------------------------------------------------------------
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163 * spotdesc
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164 * spot descriptor table
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165 *
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166 * history:
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167 * 1.0.1 - base explicitly upon sequence #1.0.1
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168 * 1.0.2 - added alternate taps for in_read_type and in_read_len
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169 */
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170 table INSDC:SRA:tbl:spotdesc #1.0.2 = INSDC:tbl:sequence #1.0.1
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171 {
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172 /* NREADS
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173 * describes the number of reads within spot
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174 */
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175 extern column U8 NREADS = out_nreads;
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176
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177
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178 /* SPOT_LEN
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179 * length of sequence
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180 * FIXED_SPOT_LEN
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181 * non-zero if sequence length is fixed throughout table
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182 */
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183 readonly column INSDC:coord:len SPOT_LEN = spot_len;
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184 readonly column INSDC:coord:len FIXED_SPOT_LEN = fixed_spot_len;
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185
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186
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187 /* TRIM_START
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188 * TRIM_LEN
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189 * define the spot segment after applying trimming
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190 * trimming may be based upon technical segments and read quality
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191 */
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192 readonly column INSDC:coord:zero TRIM_START
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193 = trim_start
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194 | < INSDC:coord:zero> echo < 0 > ();
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195 readonly column INSDC:coord:one TRIM_START
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196 = ( INSDC:coord:one ) < I32 > sum < 1 > ( trim_start )
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197 | < INSDC:coord:one> echo < 1 > ();
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198 readonly column INSDC:coord:len TRIM_LEN
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199 = trim_len
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200 | spot_len;
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201
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202
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203 /* LABEL
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204 * LABEL_START, LABEL_LEN
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205 * column pair for writing read labels
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206 * the label text for all reads is concatenated to form the LABEL row
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207 * starting coordinates and lengths delineate labels by read
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208 *
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209 * NB - row length for LABEL_START/LEN === NREADS,
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210 * row length for LABEL === SUM ( LABEL_LEN [ n ] ) for NREADS
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211 */
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212 extern column ascii LABEL = out_label;
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213 extern column INSDC:coord:zero LABEL_START = out_label_start;
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214 extern column INSDC:coord:len LABEL_LEN = out_label_len;
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215
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216 // 16-bit versions
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217 readonly column U16 LABEL_START = cast ( out_label_start );
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218 readonly column U16 LABEL_LEN = cast ( out_label_len );
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219
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220
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221 /* READ_TYPE
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222 * binary values giving type of a read
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223 *
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224 * NB - row length === NREADS
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225 */
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226 extern default column INSDC:SRA:xread_type READ_TYPE = out_read_type;
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227
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228 INSDC:SRA:xread_type in_read_type
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229 = READ_TYPE
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230 | _alt_in_read_type;
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231
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232 readonly column INSDC:SRA:read_type READ_TYPE
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233 = out_read_type
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234 | < INSDC:SRA:xread_type, INSDC:SRA:read_type > map < [ 0,1,2,3,4,5,6,7 ], [ 0,1,0,1,0,1,0,1 ] > ( out_read_type );
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235
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236
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237 /* READ_START
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238 * READ_LEN
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239 * define starting coordinates and length of read segments
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240 *
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241 * NB - row length === NREADS
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242 */
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243 extern default column INSDC:coord:zero READ_START
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244 = out_read_start;
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245 extern column INSDC:coord:one READ_START
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246 = ( INSDC:coord:one ) < I32 > sum < 1 > ( out_read_start );
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247 extern column INSDC:coord:len READ_LEN = out_read_len;
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248
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249 // 16-bit versions
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250 readonly column U16 READ_START = cast ( out_read_start );
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251 readonly column U16 READ_LEN = cast ( out_read_len );
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252
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253 INSDC:coord:len in_read_len
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254 = READ_LEN
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255 | _alt_in_read_len;
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256
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257
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258 /* READ_FILTER
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259 * bits indicate usability of sequence
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260 * always available
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261 */
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262 extern column INSDC:SRA:read_filter READ_FILTER
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263 = out_rd_filter
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264 | < INSDC:SRA:read_filter > echo < SRA_READ_FILTER_PASS > ( out_read_start );
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265
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266 // RD_FILTER - only available if physical column is present
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267 extern readonly column INSDC:SRA:read_filter RD_FILTER = out_rd_filter;
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268
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269
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270 /* spot_len is used internally */
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271 INSDC:coord:len spot_len
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272 = base_space_spot_len
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273 | color_space_spot_len
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274 | align_spot_len;
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275 INSDC:coord:len fixed_spot_len
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276 = static_fixed_spot_len
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277 | base_space_fixed_spot_len
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278 | color_space_fixed_spot_len;
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279
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280
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281 /* INSDC:tbl:sequence inherited virtual productions
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282 * out_2cs_packed
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283 * out_2na_packed
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284 */
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285
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286 /* INSDC:SRA:tbl:spotdesc productions
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287 * trim_len
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288 * out_label
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289 * out_nreads
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290 * trim_start
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291 * out_read_len
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292 * out_label_len
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293 * out_rd_filter
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294 * out_read_type
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295 * out_read_start
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296 * out_label_start
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297 * static_fixed_spot_len
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298 */
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299 };
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300
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301 /*--------------------------------------------------------------------------
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302 * stats
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303 * run and spot-group statistics
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304 *
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305 * history:
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306 * 1.1.0 - added CMP_BASE_COUNT
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307 */
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308 table INSDC:SRA:tbl:stats #1.1
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309 {
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310 readonly column INSDC:SRA:spotid_t MIN_SPOT_ID
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311 = min_spot_id
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312 | < INSDC:SRA:spotid_t > echo < 1 > ();
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313 readonly column INSDC:SRA:spotid_t MAX_SPOT_ID
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314 = max_spot_id
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315 | cast ( spot_count );
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316 readonly column U64
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317 SPOT_COUNT = spot_count;
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318 readonly column U64
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319 BASE_COUNT = base_count;
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320 readonly column U64
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321 BIO_BASE_COUNT = bio_base_count;
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322 readonly column U64 CMP_BASE_COUNT
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323 = cmp_base_count
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324 | base_count;
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325
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326 U8 stats_dummy = in_stats_bin;
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327
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328 /* INSDC:SRA:tbl:stats productions
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329 * base_count
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330 * spot_count
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331 * max_spot_id
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332 * min_spot_id
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333 * in_stats_bin
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334 * bio_base_count
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335 * cmp_base_count
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336 */
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337 };
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338
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339 /*--------------------------------------------------------------------------
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340 * sra
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341 * the INSDC SRA table
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342 *
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343 * history:
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344 * 1.0.1 - base explicitly upon spotname #1.0.1
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345 * 1.0.2 - base explicitly upon sequence #1.0.1, spotdesc #1.0.1
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346 * 1.0.3 - base upon spotdesc #1.0.2
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347 */
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348
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349 // platform constants from <insdc/sra.h>
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350 typedef U8 INSDC:SRA:platform_id;
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351 const INSDC:SRA:platform_id SRA_PLATFORM_UNDEFINED = 0;
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352 const INSDC:SRA:platform_id SRA_PLATFORM_454 = 1;
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353 const INSDC:SRA:platform_id SRA_PLATFORM_ILLUMINA = 2;
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354 const INSDC:SRA:platform_id SRA_PLATFORM_ABSOLID = 3;
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355 const INSDC:SRA:platform_id SRA_PLATFORM_COMPLETE_GENOMICS = 4;
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356 const INSDC:SRA:platform_id SRA_PLATFORM_HELICOS = 5;
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357 const INSDC:SRA:platform_id SRA_PLATFORM_PACBIO_SMRT = 6;
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358 const INSDC:SRA:platform_id SRA_PLATFORM_ION_TORRENT = 7;
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359 const INSDC:SRA:platform_id SRA_PLATFORM_CAPILLARY = 8;
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360 const INSDC:SRA:platform_id SRA_PLATFORM_OXFORD_NANOPORE = 9;
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361
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362 table INSDC:SRA:tbl:sra #1.0.3 =
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363 INSDC:tbl:sequence #1.0.1, INSDC:SRA:tbl:spotname #1.0.1,
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364 INSDC:SRA:tbl:spotdesc #1.0.2, INSDC:SRA:tbl:stats #1.1.0
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365 {
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366 /* PLATFORM
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367 * platform description
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368 * one version returns a constant defined above
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369 * while the other returns a textual representation
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370 */
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371 extern column INSDC:SRA:platform_id PLATFORM
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372 = .PLATFORM
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373 | out_platform;
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374 readonly column ascii PLATFORM
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375 = platform_name;
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376
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377 physical column
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378 < INSDC:SRA:platform_id > zip_encoding .PLATFORM = PLATFORM;
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379
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380
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381 /* SPOT_ID
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382 * reports spot id of current row
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383 */
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384 extern column INSDC:SRA:spotid_t SPOT_ID
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385 = < INSDC:SRA:spotid_t > add_row_id ( .SPOT_ID )
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386 | cast ( rowid_64 );
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387 I64 rowid_64 = row_id ();
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388
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389 physical column < INSDC:SRA:spotid_t > izip_encoding .SPOT_ID
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390 = < INSDC:SRA:spotid_t > sub_row_id ( SPOT_ID );
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391
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392
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393 /* SPOT_GROUP
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394 * a name denoting group membership, ''
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395 * used for "barcode" support
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396 */
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397 extern column ascii SPOT_GROUP
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398 = out_spot_group
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399 | .SPOT_GROUP
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400 | < ascii > echo < '' > ();
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401
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402 ascii in_spot_group = SPOT_GROUP;
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403
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404 physical column
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405 < ascii > zip_encoding < Z_DEFAULT_STRATEGY, Z_BEST_SPEED > .SPOT_GROUP = in_spot_group;
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406
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407
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408 /* INSDC:tbl:sequence inherited virtual productions
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409 * cs_native
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410 * in_cs_key
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411 * out_cs_key
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412 * out_signal
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413 * in_dna_text
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414 * out_2cs_bin
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415 * out_2na_bin
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416 * out_4na_bin
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417 * out_dna_text
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418 * out_x2cs_bin
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419 * out_x2na_bin
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420 * in_color_text
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421 * out_2cs_packed
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422 * out_2na_packed
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423 * out_4na_packed
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424 * out_color_text
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425 * out_qual_phred
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426 * out_color_matrix
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427 */
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428
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429 /* INSDC:SRA:tbl:spotcoord inherited virtual productions
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430 * out_x_coord
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431 * out_y_coord
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432 */
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433
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434 /* INSDC:SRA:tbl:spotname inherited virtual productions
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435 * out_name_fmt
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436 * out_spot_name
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437 * spot_ids_found
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438 */
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439
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440 /* INSDC:SRA:tbl:spotdesc inherited productions
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441 * trim_len
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442 * out_label
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443 * out_nreads
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444 * trim_start
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445 * out_read_len
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446 * out_label_len
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447 * out_rd_filter
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448 * out_read_type
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449 * out_read_start
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450 * out_label_start
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451 * static_fixed_spot_len
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452 */
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453
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454 /* INSDC:SRA:tbl:stats inherited productions
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455 * base_count
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456 * spot_count
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457 * max_spot_id
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458 * min_spot_id
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459 * in_stats_bin
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460 * bio_base_count
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461 */
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462
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463 /* INSDC:SRA:tbl:sra productions
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464 * out_platform
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465 * platform_name
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466 */
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467 };