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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/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 * NCBI 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 'vdb/vdb.vschema';
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33 include 'ncbi/seq.vschema';
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34 include 'ncbi/spotname.vschema';
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35 include 'insdc/sra.vschema';
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36 include 'ncbi/stats.vschema';
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37
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38
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39 /*--------------------------------------------------------------------------
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40 * types
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41 */
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42
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43
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44 /* Segment - DEPRECATED
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45 * a ( start, len ) pair where start is a zero-based, unsigned coordinate
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46 */
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47 typedef U16 NCBI:SRA:Segment [ 2 ];
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48
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49
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50 /* SpotDesc - DEPRECATED
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51 * uint16_t spot_len;
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52 * uint16_t fixed_len;
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53 * uint16_t signal_len;
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54 * uint16_t clip_qual_right;
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55 * uint8_t num_reads;
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56 * uint8_t align [ 7 ];
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57 */
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58 typedef B8 NCBI:SRA:SpotDesc [ 16 ];
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59
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60
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61 /* ReadDesc - DEPRECATED
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62 * SRASegment { uint16_t start, len; } seg;
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63 * uint8_t type;
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64 * char cs_key;
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65 * char label [ 74 ];
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66 */
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67 typedef B8 NCBI:SRA:ReadDesc [ 80 ];
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68
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69
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70 // some types have been moved to INSDC
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71 alias INSDC:SRA:platform_id NCBI:SRA:platform_id;
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72 alias INSDC:SRA:read_type NCBI:SRA:read_type;
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73 alias INSDC:SRA:read_filter NCBI:SRA:read_filter;
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74
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75 typedef NCBI:fsamp4 NCBI:SRA:rotated_fsamp4, NCBI:SRA:swapped_fsamp4;
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76
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77 // 16-bit POSITION type
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78 typedef U16 NCBI:SRA:pos16;
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79
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80
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81 /*--------------------------------------------------------------------------
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82 * functions
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83 */
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84
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85 /* bio_start
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86 * searches through read_type vector
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87 * returns the 0-based starting coordinate of first biological read
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88 *
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89 * "read_start" [ DATA ] - vector of read start coordinates
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90 *
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91 * "read_type" [ DATA ] - vector of read types
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92 */
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93 extern function INSDC:coord:zero
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94 NCBI:SRA:bio_start #1 ( INSDC:coord:zero read_start, INSDC:SRA:xread_type read_type );
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95
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96
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97 /* bio_end
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98 * searcehes through read_type vector
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99 * returns the 0 based ending coording (either inclusive or exclusive) of last
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100 * biological read
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101 *
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102 * "read_start" [ DATA ] - vector of read start coordinates
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103 *
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104 * "read_type" [ DATA ] - vector of read types
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105 *
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106 * "read_len" [ DATA ] - vector of read lengths
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107 */
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108 extern function INSDC:coord:zero
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109 NCBI:SRA:bio_end #1 < bool inclusive > ( INSDC:coord:zero read_start, INSDC:SRA:xread_type read_type, INSDC:coord:len read_len );
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110
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111
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112 /* fix_read_seg
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113 */
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114 extern function INSDC:coord:len [ 2 ]
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115 NCBI:SRA:fix_read_seg #1 ( U16 [ 2 ] rd_seg, INSDC:coord:len spot_len );
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116
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117
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118 /* make_spot_desc
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119 * assembles several bits of information together into a "C" structure
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120 *
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121 * "spot_len" [ DATA ] - computed spot length value
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122 *
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123 * "fixed_len" [ DATA, DFLT ZERO ] - the stated fixed length of all spots
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124 * or zero if not fixed length
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125 *
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126 * "sig_len" [ DATA, DFLT ZERO ] - the length of signal/intensity data
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127 * or zero if not present
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128 *
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129 * "trim_start" [ DATA ] - the first base included in the trim segment
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130 *
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131 * "trim_len" [ DATA ] - the length of the trim segment
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132 *
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133 * "num_reads" [ DATA ] - 1..n value
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134 */
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135 extern function NCBI:SRA:SpotDesc NCBI:SRA:make_spot_desc #1 ( INSDC:coord:len spot_len,
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136 INSDC:coord:len fixed_len, INSDC:coord:len sig_len, INSDC:coord:zero trim_start,
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137 INSDC:coord:len trim_len, U8 num_reads );
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138
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139
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140 /* make_read_desc
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141 * assembles several bits of information together into a "C" structure
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142 * in theory resultant segments may intersect other read segments or leave holes in spot.
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143 *
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144 * "num_reads" [ DATA ] - value indicating the resulting row-length of output
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145 *
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146 * "read_start" [ DATA ] - ordered starting coordinates for each read
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147 * not required to be sequential.
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148 *
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149 * "read_len" [ DATA ] - ordered lengths of each read. may be zero when
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150 * read has been described but is not identified in spot.
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151 *
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152 * "read_type" [ DATA ] - ordered type id describing each read
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153 *
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154 * "read_filt" [ DATA ] - ordered read filters
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155 *
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156 * "cs_key" [ DATA ] - ordered color-space keys
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157 *
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158 * "label_start" [ DATA ] - ordered starting coordinates for each label
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159 * "label_len" [ DATA ] - ordered lengths of each label
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160 *
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161 * "label" [ DATA ] - complete sequence of label characters, possibly empty
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162 * individual read labels are identified as {start,len} pairs
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163 */
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164 extern function NCBI:SRA:ReadDesc NCBI:SRA:make_read_desc #1 ( U8 num_reads,
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165 INSDC:coord:zero read_start, INSDC:coord:len read_len, INSDC:SRA:xread_type read_type,
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166 INSDC:SRA:read_filter read_filt, INSDC:dna:text cs_key,
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167 INSDC:coord:zero label_start, INSDC:coord:len label_len, ascii label );
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168
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169
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170 /* rotate
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171 * rotate a quadruple by called base
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172 * now normally replaced by swap
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173 *
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174 * "T" [ TYPE ] - element type of quadruple to be rotated
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175 *
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176 * "encoding" [ CONST ] - when true, rotate input left until corresponding
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177 * element is in slot 0. when false, rotate input right to restore original
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178 * order.
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179 *
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180 * "in" [ DATA ] - data to be rotated, qualities, signal, intensities...
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181 *
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182 * "called" [ DATA ] - {0..3} or {0..4} binary representation of called bases or colors
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183 */
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184 extern function < type T >
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185 T NCBI:SRA:rotate #1 < bool encoding > ( T in, U8 called );
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186
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187
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188 /* swap
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189 * swap element 0 and the called element
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190 * used to ensure that the called element is in slot 0
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191 *
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192 * "T" [ TYPE ] - element type of quadruple to be swapped
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193 *
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194 * "in" [ DATA ] - data to be swapped, qualities, signal, intensities...
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195 *
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196 * "called" [ DATA ] - {0..3} or {0..4} binary representation of called bases or colors
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197 */
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198 extern function < type T >
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199 T NCBI:SRA:swap #1 ( T in, U8 called );
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200
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201
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202 /* normalize
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203 * denormalize
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204 *
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205 * "T" [ TYPE ] - element type of quadruple to be [de]normalized
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206 *
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207 * "intensity" [ DATA ] - intensity data
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208 *
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209 * "called" [ DATA ] - {0..3} or {0..4} binary representation of called bases or colors
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210 */
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211 extern function < type T >
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212 T NCBI:SRA:normalize #1 ( T intensity, U8 called );
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213
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214 extern function < type T >
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215 T NCBI:SRA:denormalize #1 ( T intensity, U8 called );
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216
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217
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218 /* make_position
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219 * return a synthesized position row with 1-1 correspondence
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220 *
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221 * "T" [ TYPE ] - position type being generated
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222 *
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223 * "start" [ CONST ] - either 0 or 1, depending upon the coordinate system
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224 *
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225 * "bases" [ DATA ] - the actual row of bases. the output row
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226 * will be the same length, but with synthesized data
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227 */
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228 extern function < type T >
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229 T NCBI:SRA:make_position #1 < T start > ( any bases );
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230
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231 /* fsamp4 compression
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232 * performs compression individually
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233 * on called channel and alternate channels
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234 */
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235 function NCBI:SRA:swapped_fsamp4 NCBI:SRA:fsamp4:decode #2 ( merged_fmt in )
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236 {
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237 fzip_fmt cmp0 = split < 0 > ( in );
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238 fzip_fmt cmp123 = split < 1 > ( in );
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239 F32 ch0 = funzip ( cmp0 );
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240 F32 ch123a = funzip ( cmp123 );
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241 F32[3] ch123 = redimension ( ch123a );
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242 return ( NCBI:SRA:swapped_fsamp4 ) < F32 > paste ( ch0, ch123 );
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243 }
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244
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245 function merged_fmt NCBI:SRA:fsamp4:encode #2 < U32 called, U32 alt > ( NCBI:SRA:swapped_fsamp4 in )
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246 {
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247 F32 ch0 = < F32 > cut < 0 > ( in );
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248 F32[3] ch123 = < F32 > cut < 1, 2, 3 > ( in );
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249 fzip_fmt cmp0 = fzip < called > ( ch0 );
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250 F32 ch123a = redimension ( ch123 );
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251 fzip_fmt cmp123 = fzip < alt > ( ch123a );
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252 return merge ( cmp0, cmp123 );
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253 }
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254
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255
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256 /*--------------------------------------------------------------------------
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257 * spotdesc
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258 * NCBI implementation productions
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259 */
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260
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261 /* history:
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262 * 1.0.1 - base explicitly upon sequence #1.0.1, spotdesc #1.0.1
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263 * 1.0.2 - spotdesc #1.0.2
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264 */
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265 table NCBI:SRA:tbl:spotdesc_nocol #1.0.2 = INSDC:tbl:sequence #1.0.1, INSDC:SRA:tbl:spotdesc #1.0.2
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266 {
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267 /* LABEL_SEG
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268 */
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269 readonly column NCBI:SRA:Segment LABEL_SEG
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270 = out_label_seg
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271 | cast ( out_label_seg32 )
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272 | cast ( _out_label_seg32 );
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273 U32 _out_label_startU32 = ( U32 ) out_label_start;
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274 U32 [ 2 ] _out_label_seg32 = < U32 > paste ( _out_label_startU32, out_label_len );
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275
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276
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277 /* READ_SEG
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278 */
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279 readonly column NCBI:SRA:Segment READ_SEG
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280 = out_read_seg
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281 | cast ( out_read_seg32 )
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282 | cast ( _out_read_seg32 );
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283 U32 _out_read_startU32 = ( U32 ) out_read_start;
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284 U32 [ 2 ] _out_read_seg32 = < U32 > paste ( _out_read_startU32, out_read_len );
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285
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286
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287 /* READ_DESC
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288 */
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289 readonly column NCBI:SRA:ReadDesc READ_DESC
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290 = NCBI:SRA:make_read_desc ( out_nreads, out_read_start, out_read_len,
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291 out_read_type, _out_rd_filter, out_cs_key, _out_label_start, _out_label_len, _out_label );
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292 INSDC:SRA:read_filter _out_rd_filter
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293 = out_rd_filter
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294 | < INSDC:SRA:read_filter > echo < SRA_READ_FILTER_PASS > ( out_read_start );
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295 ascii _out_label
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296 = out_label
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297 | < ascii > echo < '' > ();
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298 INSDC:coord:zero _out_label_start
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299 = out_label_start
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300 | < INSDC:coord:zero > echo < 0 > ( out_read_start );
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301 INSDC:coord:len _out_label_len
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302 = out_label_len
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303 | < INSDC:coord:len > echo < 0 > ( out_read_start );
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304
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305 /* SPOT_DESC
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306 */
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307 readonly column NCBI:SRA:SpotDesc SPOT_DESC
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308 = NCBI:SRA:make_spot_desc ( spot_len, fixed_spot_len, signal_len,
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309 trim_start, trim_len, out_nreads );
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310
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311 /* SIGNAL_LEN
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312 * normally the same as spot length when present,
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313 * but in some cases ( e.g. 454 ) it may be different
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314 */
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315 readonly column INSDC:coord:len SIGNAL_LEN
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316 = signal_len;
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317 readonly column U16 SIGNAL_LEN
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318 = cast ( signal_len );
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319
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320
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321 /* INSDC:SRA:tbl:spotdesc inherited productions
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322 * trim_len
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323 * out_label
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324 * out_nreads
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325 * trim_start
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326 * out_read_len
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327 * out_label_len
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328 * out_rd_filter
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329 * out_read_type
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330 * out_read_start
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331 * out_label_start
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332 * static_fixed_spot_len
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333 */
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334
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335 /* NCBI:SRA:tbl:spotdesc_nocol productions
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336 * out_read_seg
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337 * out_label_seg
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338 * out_read_seg32
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339 * out_label_seg32
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340 */
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341 };
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342
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343 /* history:
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344 * 1.0.1 - base explicitly upon spotdesc_nocol #1.0.1
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345 * 1.0.2 - base explicitly upon spotdesc_nocol #1.0.2
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346 */
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347 table NCBI:SRA:tbl:spotdesc_nophys #1.0.2 = NCBI:SRA:tbl:spotdesc_nocol #1.0.2
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348 {
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349 // resolve virtual productions
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350 U8 out_nreads = .NREADS;
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351 ascii out_label = .LABEL;
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352 INSDC:SRA:xread_type out_read_type = .READ_TYPE;
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353 INSDC:SRA:read_filter out_rd_filter = .RD_FILTER;
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354
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355 INSDC:coord:zero out_label_start
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356 = .LABEL_START
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357 | ( INSDC:coord:zero ) < U32 > cut < 0 > ( out_label_seg32 );
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358 INSDC:coord:len out_label_len
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359 = .LABEL_LEN
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360 | ( INSDC:coord:len ) < U32 > cut < 1 > ( out_label_seg32 );
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361 U32 [ 2 ] out_label_seg32
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362 = cast ( .LABEL_SEG );
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363
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364 INSDC:coord:zero out_read_start
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365 = .READ_START
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366 | ( INSDC:coord:zero ) < U32 > cut < 0 > ( out_read_seg32 );
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367 INSDC:coord:len out_read_len
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368 = .READ_LEN
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369 | ( INSDC:coord:len ) < U32 > cut < 1 > ( out_read_seg32 );
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370 U32 [ 2 ] out_read_seg32
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371 = NCBI:SRA:fix_read_seg ( .READ_SEG, spot_len );
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372
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373
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374 /* INSDC:SRA:tbl:spotdesc inherited productions
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375 * trim_len
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376 * trim_start
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377 * out_read_type
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378 * static_fixed_spot_len
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379 */
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380
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381 /* NCBI:SRA:tbl:spotdesc_nocol inherited productions
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382 * out_read_seg
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383 * out_label_seg
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384 */
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385
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386 /* NCBI:SRA:tbl:spotdesc_nophys productions
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387 * .LABEL
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388 * .NREADS
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389 * .READ_LEN
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390 * .READ_SEG
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391 * .LABEL_LEN
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392 * .LABEL_SEG
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393 * .RD_FILTER
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394 * .READ_TYPE
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395 * .READ_START
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396 * .LABEL_START
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397 */
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398 }
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399
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400 /* history:
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401 * 1.0.1 - base explicitly upon spotdesc_nophys #1.0.1
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402 * 1.0.2 - base explicitly upon spotdesc_nophys #1.0.2
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403 */
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404 table NCBI:SRA:tbl:spotdesc #1.0.2 = NCBI:SRA:tbl:spotdesc_nophys #1.0.2
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405 {
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406 // physical column encodings
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407 // TBD - this has to be looked at, where dynamic segmentation is involved
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408 physical column < U8 > zip_encoding .NREADS = NREADS;
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409 physical column < ascii > zip_encoding .LABEL = LABEL;
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410 physical column < INSDC:coord:zero > izip_encoding .LABEL_START = LABEL_START;
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411 physical column < INSDC:coord:len > izip_encoding .LABEL_LEN = LABEL_LEN;
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412 physical column < INSDC:coord:zero > izip_encoding .READ_START = READ_START;
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413 physical column < INSDC:coord:len > izip_encoding .READ_LEN = in_read_len;
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414 physical column < INSDC:SRA:xread_type > zip_encoding .READ_TYPE = in_read_type;
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415 physical column < INSDC:SRA:read_filter > zip_encoding .RD_FILTER = READ_FILTER;
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416
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417
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418 /* INSDC:SRA:tbl:spotdesc inherited productions
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419 * trim_len
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420 * trim_start
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421 * out_read_type
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422 * static_fixed_spot_len
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423 */
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424
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425 /* NCBI:SRA:tbl:spotdesc_nocol inherited productions
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426 * out_read_seg
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427 * out_label_seg
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428 */
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429 };
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430
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431
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432 /*--------------------------------------------------------------------------
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433 * pos
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434 * synthetic POSITION column on read
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435 *
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436 * history:
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437 * 1.0.1 - base explicitly upon sequence #1.0.1
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438 */
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439
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440 table NCBI:SRA:tbl:pos #1.0.1 = INSDC:tbl:sequence #1.0.1
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441 {
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442 INSDC:position:one out_position
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443 = < INSDC:position:one > NCBI:SRA:make_position < 1 > ( out_2na_packed )
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444 | < INSDC:position:one > NCBI:SRA:make_position < 1 > ( out_2cs_packed );
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445 NCBI:SRA:pos16 out_position16
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446 = < NCBI:SRA:pos16 > NCBI:SRA:make_position < 1 > ( out_2na_packed )
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447 | < NCBI:SRA:pos16 > NCBI:SRA:make_position < 1 > ( out_2cs_packed );
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448 };
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449
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450
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451 /*--------------------------------------------------------------------------
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452 * sra
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453 * the NCBI SRA table
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454 */
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455
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456 /* history:
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457 * 1.0.1 - base explicitly upon sra #1.0.1
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458 * 1.0.2 - base explicitly upon sra #1.0.2, spotdesc_nocol #1.0.1
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459 * 1.0.3 - base explicitly upon sra #1.0.3, spotdesc_nocol #1.0.2
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460 */
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461 table NCBI:SRA:tbl:sra_nopos #1.0.3 = INSDC:SRA:tbl:sra #1.0.3, NCBI:SRA:tbl:spotdesc_nocol #1.0.2
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462 {
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463 // v1 declares the POSITION column for all tables
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464 // but leaves all physical columns unstated
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465
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466 /* POSITION
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467 * 1-based coordinates
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468 * describes a base's position on signal
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469 */
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470 column INSDC:position:one POSITION = out_position;
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471 readonly column NCBI:SRA:pos16 POSITION = out_position16;
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472
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473 // zero-based coordinates available upon request
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474 readonly column INSDC:position:zero POSITION
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475 = ( INSDC:position:zero ) < I32 > diff < 1 > ( out_position );
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476
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477 // statistics
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478 U64 base_count
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479 = < U64 > meta:value < "BASE_COUNT" > ();
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480 U64 spot_count
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481 = < U64 > meta:value < ".seq/spot" > ()
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482 | < U64 > meta:value < ".seq" > () ;
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483
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484
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485 /* INSDC:tbl:sequence inherited productions
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486 * cs_native
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487 * in_cs_key
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488 * out_cs_key
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489 * out_signal
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490 * in_dna_text
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491 * out_2cs_bin
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492 * out_2na_bin
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493 * out_4na_bin
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494 * out_dna_text
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495 * out_x2cs_bin
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496 * out_x2na_bin
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497 * in_color_text
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498 * out_2cs_packed
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499 * out_2na_packed
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500 * out_4na_packed
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diff changeset
501 * out_color_text
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diff changeset
502 * out_qual_phred
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diff changeset
503 * out_color_matrix
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504 */
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diff changeset
505
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506 /* INSDC:SRA:tbl:spotname inherited productions
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diff changeset
507 * out_x_coord
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diff changeset
508 * out_y_coord
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diff changeset
509 * out_name_fmt
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diff changeset
510 * out_spot_name
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diff changeset
511 * spot_ids_found
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512 */
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diff changeset
513
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diff changeset
514 /* INSDC:SRA:tbl:spotdesc inherited productions
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parents:
diff changeset
515 * trim_len
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diff changeset
516 * out_label
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diff changeset
517 * out_nreads
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diff changeset
518 * trim_start
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diff changeset
519 * out_read_len
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diff changeset
520 * out_label_len
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diff changeset
521 * out_rd_filter
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diff changeset
522 * out_read_type
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diff changeset
523 * out_read_start
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diff changeset
524 * out_label_start
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diff changeset
525 * static_fixed_spot_len
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526 */
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527
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528 /* INSDC:SRA:tbl:stats inherited productions
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diff changeset
529 * max_spot_id
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diff changeset
530 * min_spot_id
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diff changeset
531 * in_stats_bin
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diff changeset
532 * bio_base_count
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533 */
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534
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535 /* INSDC:SRA:tbl:sra inherited productions
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diff changeset
536 * out_platform
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diff changeset
537 * platform_name
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538 */
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539
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540 /* NCBI:SRA:tbl:spotdesc_nocol inherited productions
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parents:
diff changeset
541 * out_read_seg
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diff changeset
542 * out_label_seg
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diff changeset
543 * out_read_seg32
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parents:
diff changeset
544 * out_label_seg32
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545 */
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546
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diff changeset
547 /* NCBI:SRA:tbl:sra_nopos productions
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diff changeset
548 * out_position
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549 * out_position16
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550 */
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551 };
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552
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diff changeset
553 /* history:
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charles_s_test
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diff changeset
554 * 1.0.1 - base explicitly upon sra #1.0.1
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diff changeset
555 * 1.0.2 - base explicitly upon sra_nopos #1.0.2, pos #1.0.1
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diff changeset
556 * 1.0.3 - base explicitly upon sra_nopos #1.0.3
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diff changeset
557 */
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diff changeset
558 table NCBI:SRA:tbl:sra #1.0.3 = NCBI:SRA:tbl:sra_nopos #1.0.3, NCBI:SRA:tbl:pos #1.0.1
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diff changeset
559 {
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diff changeset
560 // the POSITION column is synthesized for all contemporary platforms but 454
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diff changeset
561
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diff changeset
562 /* INSDC:tbl:sequence inherited productions
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diff changeset
563 * cs_native
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diff changeset
564 * in_cs_key
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diff changeset
565 * out_cs_key
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diff changeset
566 * out_signal
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diff changeset
567 * in_dna_text
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diff changeset
568 * out_2cs_bin
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diff changeset
569 * out_2na_bin
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diff changeset
570 * out_4na_bin
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diff changeset
571 * out_dna_text
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diff changeset
572 * out_x2cs_bin
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diff changeset
573 * out_x2na_bin
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diff changeset
574 * in_color_text
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diff changeset
575 * out_2cs_packed
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diff changeset
576 * out_2na_packed
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diff changeset
577 * out_4na_packed
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charles_s_test
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diff changeset
578 * out_color_text
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diff changeset
579 * out_qual_phred
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diff changeset
580 * out_color_matrix
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581 */
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diff changeset
582
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diff changeset
583 /* INSDC:SRA:tbl:spotname inherited productions
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diff changeset
584 * out_x_coord
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diff changeset
585 * out_y_coord
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diff changeset
586 * out_name_fmt
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diff changeset
587 * out_spot_name
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diff changeset
588 * spot_ids_found
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589 */
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590
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diff changeset
591 /* INSDC:SRA:tbl:spotdesc inherited productions
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diff changeset
592 * trim_len
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diff changeset
593 * out_label
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diff changeset
594 * out_nreads
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diff changeset
595 * trim_start
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diff changeset
596 * out_read_len
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diff changeset
597 * out_label_len
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diff changeset
598 * out_rd_filter
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diff changeset
599 * out_read_type
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diff changeset
600 * out_read_start
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diff changeset
601 * out_label_start
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diff changeset
602 * static_fixed_spot_len
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diff changeset
603 */
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diff changeset
604
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diff changeset
605 /* INSDC:SRA:tbl:stats inherited productions
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diff changeset
606 * max_spot_id
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diff changeset
607 * min_spot_id
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diff changeset
608 * in_stats_bin
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diff changeset
609 * bio_base_count
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610 */
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diff changeset
611
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diff changeset
612 /* INSDC:SRA:tbl:sra inherited productions
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diff changeset
613 * out_platform
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diff changeset
614 * platform_name
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615 */
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616
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diff changeset
617 /* NCBI:SRA:tbl:spotdesc_nocol inherited productions
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diff changeset
618 * out_read_seg
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diff changeset
619 * out_label_seg
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620 * out_read_seg32
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diff changeset
621 * out_label_seg32
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622 */
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623 };
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624
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625
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626 /* v2 consolidates many of the auxiliary columns into a single treatment
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diff changeset
627 * left out are reads, qualities and platform-specific columns
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diff changeset
628 *
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diff changeset
629 * history:
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diff changeset
630 * 2.1.2 - base upon sra #1.0.3, spotdesc #1.0.2, stats #1.1.2
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diff changeset
631 */
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632 table NCBI:SRA:tbl:sra_nopos #2.1.3 = INSDC:SRA:tbl:sra #1.0.3,
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diff changeset
633 NCBI:SRA:tbl:skeyname #3.0.1, NCBI:SRA:tbl:spotdesc #1.0.2, NCBI:SRA:tbl:stats #1.2.0
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634 {
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635 // this is already specified in INSDC:SRA:tbl:sra #1
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diff changeset
636 // but putting it here will quiet down outputs
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diff changeset
637 INSDC:SRA:platform_id out_platform = .PLATFORM;
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diff changeset
638
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639 column INSDC:position:one POSITION
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diff changeset
640 = out_position;
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641 readonly column NCBI:SRA:pos16 POSITION
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diff changeset
642 = cast ( _clip_position );
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643 INSDC:position:one _clip_position
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644 = < INSDC:position:one > clip < 0, 0xFFFF > ( out_position );
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645 readonly column INSDC:position:zero POSITION
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diff changeset
646 = ( INSDC:position:zero ) < I32 > diff < 1 > ( out_position );
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647
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648
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649 /* INSDC:tbl:sequence inherited productions
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diff changeset
650 * cs_native
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651 * in_cs_key
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652 * out_cs_key
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653 * out_signal
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654 * in_dna_text
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655 * out_2cs_bin
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656 * out_2na_bin
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657 * out_4na_bin
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658 * out_dna_text
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659 * out_x2cs_bin
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660 * out_x2na_bin
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661 * in_color_text
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662 * out_2cs_packed
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663 * out_2na_packed
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664 * out_4na_packed
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665 * out_color_text
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666 * out_qual_phred
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667 * out_color_matrix
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668 */
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669
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670 /* INSDC:SRA:tbl:spotdesc inherited productions
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671 * trim_len
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672 * trim_start
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673 * out_read_type
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674 * static_fixed_spot_len
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675 */
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676
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677 /* INSDC:SRA:tbl:stats inherited productions
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678 * in_stats_bin
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679 */
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680
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681 /* INSDC:SRA:tbl:sra inherited productions
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682 * out_platform
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683 * platform_name
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684 */
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685
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686 /* NCBI:SRA:tbl:skeyname inherited productions
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687 * in_spot_name_tok
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688 */
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689
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690 /* NCBI:SRA:tbl:spotdesc_nocol inherited productions
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691 * out_read_seg
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692 * out_label_seg
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693 */
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694
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695 /* NCBI:SRA:tbl:sra_nopos productions
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696 * out_position
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697 */
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698 };
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699
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diff changeset
700 /* most platforms don't have a native POSITION
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701 * mix in "pos" table to synthesize it
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702 *
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703 * history:
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diff changeset
704 * 2.1.2 - base upon sra#1.0.3, spotdesc #1.0.2, stats #1.1.2
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diff changeset
705 */
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diff changeset
706 table NCBI:SRA:tbl:sra #2.1.3 = INSDC:SRA:tbl:sra #1.0.3,
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707 NCBI:SRA:tbl:skeyname #3.0.1, NCBI:SRA:tbl:spotdesc #1.0.2,
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diff changeset
708 NCBI:SRA:tbl:stats #1.2.0, NCBI:SRA:tbl:pos #1.0.1
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diff changeset
709 {
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diff changeset
710 readonly column INSDC:position:one POSITION
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charles_s_test
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diff changeset
711 = out_position;
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712 readonly column NCBI:SRA:pos16 POSITION
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713 = out_position16;
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714 readonly column INSDC:position:zero POSITION
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diff changeset
715 = ( INSDC:position:zero ) < I32 > diff < 1 > ( out_position );
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diff changeset
716
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diff changeset
717
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diff changeset
718 /* INSDC:tbl:sequence inherited productions
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diff changeset
719 * cs_native
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diff changeset
720 * in_cs_key
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diff changeset
721 * out_cs_key
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diff changeset
722 * out_signal
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diff changeset
723 * in_dna_text
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diff changeset
724 * out_2cs_bin
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diff changeset
725 * out_2na_bin
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diff changeset
726 * out_4na_bin
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diff changeset
727 * out_dna_text
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diff changeset
728 * out_x2cs_bin
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diff changeset
729 * out_x2na_bin
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diff changeset
730 * in_color_text
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diff changeset
731 * out_2cs_packed
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diff changeset
732 * out_2na_packed
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diff changeset
733 * out_4na_packed
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diff changeset
734 * out_color_text
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diff changeset
735 * out_qual_phred
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diff changeset
736 * out_color_matrix
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737 */
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738
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739 /* INSDC:SRA:tbl:spotdesc inherited productions
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diff changeset
740 * trim_len
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diff changeset
741 * trim_start
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742 * out_read_type
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743 * static_fixed_spot_len
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744 */
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745
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746 /* INSDC:SRA:tbl:stats inherited productions
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diff changeset
747 * in_stats_bin
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748 */
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749
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750 /* INSDC:SRA:tbl:sra inherited productions
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diff changeset
751 * out_platform
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diff changeset
752 * platform_name
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753 */
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diff changeset
754
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755 /* NCBI:SRA:tbl:skeyname inherited productions
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diff changeset
756 * in_spot_name_tok
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diff changeset
757 */
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758 };