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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/sra/illumina.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 Illumina 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 'ncbi/sra.vschema';
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33 include 'ncbi/spotname.vschema';
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34
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35
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36 /*--------------------------------------------------------------------------
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37 * types
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38 */
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39
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40 typedef INSDC:quality:log_odds NCBI:qual4 [ 4 ];
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41 typedef NCBI:qual4 NCBI:SRA:rotated_qual4, NCBI:SRA:swapped_qual4;
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42
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43
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44 /*--------------------------------------------------------------------------
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45 * functions
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46 */
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47
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48 /* tokenize_spot_name
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49 * scans name on input
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50 * tokenizes into parts
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51 */
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52 extern function NCBI:SRA:spot_name_token
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53 NCBI:SRA:Illumina:tokenize_spot_name #1 ( ascii name );
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54
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55
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56 /*--------------------------------------------------------------------------
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57 * NCBI:SRA:Illumina:qual4
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58 * 4-channel log-odds-ish quality
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59 */
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60
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61 /* history:
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62 * 1.0.1 - base explicitly upon updated ancestry
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63 */
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64 table NCBI:SRA:Illumina:qual4_nocol #1.0.1
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65 = INSDC:tbl:sequence #1.0.1
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66 , NCBI:tbl:log_odds_quality_nocol #1.0.1
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67 {
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68 /* QUALITY
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69 * 4-channel quality column
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70 */
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71 readonly column NCBI:qual4 QUALITY = out_qual4;
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72
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73 NCBI:qual4 out_qual4
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74 = < NCBI:qual4 > NCBI:SRA:swap ( out_qual4_swapped, read_unpack )
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75 | < NCBI:qual4 > NCBI:SRA:rotate < false > ( out_qual4_rotated, read_unpack );
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76
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77
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78 /* single-channel output
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79 * convert 4-channel log-odds to single channel
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80 * must retain n-encoding, which was intended to be the 4-channel pattern
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81 * ( -5, -5, -5, -5 ) and a base of 'A'
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82 */
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83
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84 // first, extract quality for called base
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85 INSDC:quality:log_odds out_qual1_ch0
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86 = < INSDC:quality:log_odds> cut < 0 > ( out_qual4_swapped )
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87 | < INSDC:quality:log_odds> cut < 0 > ( out_qual4_rotated );
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88
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89 // clip it to -5 and above
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90 INSDC:quality:log_odds out_qual1_clip
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91 = < INSDC:quality:log_odds > clip < -5, 127 > ( out_qual1_ch0 );
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92
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93 // convert 4 channel to single 32-bit value
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94 U32 out_qual4_32
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95 = redimension ( out_qual4_swapped )
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96 | redimension ( out_qual4_rotated );
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97
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98 // detect ( -5, -5, -5, -5 ) and introduce a -6 value into log-odds
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99 // this is treated as an 'N', but still not ready
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100 INSDC:quality:log_odds out_qual1_fives
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101 = < U32, INSDC:quality:log_odds > map < 0xFBFBFBFB, -6 > ( out_qual4_32, out_qual1_clip );
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102
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103 // now slam zeros into anything that doesn't correspond to an A
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104 // essentially this leaves all of the A qualities. any having -6 are really N.
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105 INSDC:quality:log_odds out_qual1_n
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106 = < U8, INSDC:quality:log_odds > map < [ 1, 2, 3 ], [ 0, 0, 0 ] > ( read_unpack, out_qual1_fives );
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107
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108 // finally, produce log-odds with n-encoded as -6
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109 INSDC:quality:log_odds out_qual_log_odds
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110 = < INSDC:quality:log_odds, INSDC:quality:log_odds > map < -6, -6 > ( out_qual1_n, out_qual1_clip );
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111
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112
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113 /* NCBI:tbl:n_encoding inherited productions
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114 * read_unpack
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115 */
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116
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117 /* NCBI:SRA:Illumina:qual4_nocol productions
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118 * out_qual4_rotated
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119 * out_qual4_swapped
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120 */
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121 };
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122
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123
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124 /* 4-channel log-odds compression
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125 */
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126
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127 // encoded type - a single byte code for 4-channel pattern
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128 typedef B8 NCBI:SRA:encoded_qual4;
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129
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130 // decoding function
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131 extern function
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132 NCBI:SRA:swapped_qual4 NCBI:SRA:qual4_decode #1 ( NCBI:SRA:encoded_qual4 in );
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133
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134 // encoding function
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135 extern function
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136 NCBI:SRA:encoded_qual4 NCBI:SRA:qual4_encode #1 ( NCBI:SRA:swapped_qual4 in );
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137
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138 // compression rules
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139 physical NCBI:SRA:swapped_qual4 NCBI:SRA:qual4_encoding #1
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140 {
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141 encode
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142 {
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143 // produce codes
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144 NCBI:SRA:encoded_qual4 encoded = NCBI:SRA:qual4_encode ( @ );
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145
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146 // gzip
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147 return zip < Z_RLE, Z_BEST_SPEED > ( encoded );
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148 }
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149
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150 decode
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151 {
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152 // gunzip
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153 NCBI:SRA:encoded_qual4 unzipped = unzip ( @ );
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154
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155 // inflate to swapped
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156 return NCBI:SRA:qual4_decode ( unzipped );
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157 }
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158 }
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159
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160 /* history:
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161 * 1.0.1 - base upon updated qual4_nocol
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162 */
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163 table NCBI:SRA:Illumina:qual4 #1.0.1 = NCBI:SRA:Illumina:qual4_nocol #1.0.1
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164 {
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165 // read directly as swapped, n-encoded log_odds
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166 NCBI:SRA:swapped_qual4 out_qual4_swapped = .QUALITY;
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167
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168 /* NCBI:tbl:n_encoding inherited virtual productions
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169 * read_unpack
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170 */
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171 };
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172
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173 /* history:
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174 * 2.0.2 - base upon updated ancestry
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175 * 2.0.3 - base upon updated ancestry
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176 * 2.0.4 - base upon updated ancestry
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177 * 2.1.0 - base upon updated ancestry, added in_qual_log_odds
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178 */
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179 table NCBI:SRA:Illumina:qual4 #2.1.0
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180 = NCBI:tbl:base_space #2.0.3
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181 , NCBI:tbl:log_odds_quality_nocol #2.1.0
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182 {
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183 /* QUALITY
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184 * 4-channel log-odds
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185 */
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186 extern column NCBI:qual4 QUALITY = out_qual4;
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187
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188 NCBI:SRA:swapped_qual4 in_qual4
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189 = ( NCBI:SRA:swapped_qual4 ) < NCBI:qual4 > NCBI:SRA:swap ( QUALITY, in_x2na_bin )
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190 | ( NCBI:SRA:swapped_qual4 ) < NCBI:qual4 > NCBI:SRA:swap ( QUALITY, in_2na_bin );
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191
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192 NCBI:qual4 out_qual4
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193 = < NCBI:SRA:swapped_qual4 > NCBI:SRA:swap ( .QUALITY, out_x2na_bin );
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194
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195 physical column NCBI:SRA:qual4_encoding .QUALITY = in_qual4;
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196
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197 // feed to compressed statistics
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198 NCBI:qual4 in_stats_qual = in_qual4;
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199
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200 // single channel
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201 INSDC:quality:log_odds in_qual_log_odds
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202 = < INSDC:quality:log_odds > cut < 0 > ( in_qual4 );
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203 INSDC:quality:log_odds out_qual_log_odds
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204 = < INSDC:quality:log_odds > cut < 0 > ( .QUALITY );
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205 };
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206
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207
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208 /*--------------------------------------------------------------------------
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209 * NCBI:SRA:Illumina
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210 * Illumina SRA Platform
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211 */
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212
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213
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214 /* NCBI:SRA:Illumina:common #1
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215 * basic table interface based upon Illumina's pipelines
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216 *
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217 * history:
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218 * 1.0.1 - explictly base upon sra #1.0.1
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219 * 1.0.2 - base explicitly upon sra #1.0.2
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220 * 1.0.3 - base explicitly upon sra #1.0.3
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221 */
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222 table NCBI:SRA:Illumina:common #1.0.3 = INSDC:SRA:tbl:sra #1.0.3
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223 {
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224 // platform name is always 'ILLUMINA'
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225 ascii platform_name
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226 = < ascii > echo < "ILLUMINA" > ();
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227
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228 /* TRIMMED SEQUENCE
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229 * need to find the 0-based trim_start and trim_len
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230 */
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231 INSDC:coord:zero bio_start = NCBI:SRA:bio_start ( out_read_start, out_read_type );
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232 INSDC:coord:zero trim_start = bio_start;
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233 U32 trim_left = ( U32 ) trim_start;
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234 INSDC:coord:len trim_len = (INSDC:coord:len) < U32 > diff ( spot_len, trim_left );
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235
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236 /* COORDINATES
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237 * in addition to X and Y,
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238 * Illumina has LANE and TILE
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239 */
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240 readonly column INSDC:coord:val LANE = out_lane_coord;
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241 readonly column INSDC:coord:val TILE = out_tile_coord;
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242 };
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243
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244
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245 /*--------------------------------------------------------------------------
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246 * NCBI:SRA:Illumina:tbl:v2 #1
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247 * normalized v2 table
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248 * still has variants based upon quality type
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249 *
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250 * history:
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251 * 1.0.1 - explictly base upon sra #1.0.1 and related tables
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252 * 1.0.2 - updated ancestry
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253 * 1.0.3 - updated ancestry
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254 */
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255
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256 physical NCBI:SRA:swapped_fsamp4 NCBI:SRA:Illumina:encoding:SIGNAL #2
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257 {
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258 decode { return NCBI:SRA:fsamp4:decode #2 ( @ ); }
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259 encode { return NCBI:SRA:fsamp4:encode #2 < 14, 10 > ( @ ); }
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260 }
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261
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262 physical NCBI:fsamp4 NCBI:SRA:Illumina:encoding:NOISE #2
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263 {
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264 decode
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265 {
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266 F32 dcmp = funzip ( @ );
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267 return redimension ( dcmp );
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268 }
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269 encode
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270 {
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271 F32 ncmp = redimension ( @ );
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272 return fzip < 10 > ( ncmp );
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273 }
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274 }
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275
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276 physical NCBI:SRA:swapped_fsamp4 NCBI:SRA:Illumina:encoding:INTENSITY #2
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277 {
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278 decode { return NCBI:SRA:fsamp4:decode #2 ( @ ); }
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279 encode { return NCBI:SRA:fsamp4:encode #2 < 14, 10 > ( @ ); }
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280 }
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281
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282 // v2 base table
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283 table NCBI:SRA:Illumina:tbl:v2 #1.0.4
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284 = NCBI:SRA:tbl:sra #2.1.3
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285 , NCBI:tbl:base_space #2.0.3
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286 , NCBI:SRA:Illumina:common #1.0.3
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287 {
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288 /* NAME tokenizing and coordinates
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289 * most work happens in skeyname table
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290 * we still obtain LANE and TILE from name
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291 */
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292 INSDC:coord:val out_lane_coord = ( INSDC:coord:val )
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293 NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:L > ( _out_name, out_spot_name_tok );
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294 INSDC:coord:val out_tile_coord = ( INSDC:coord:val )
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295 NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:T > ( _out_name, out_spot_name_tok );
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296 NCBI:SRA:spot_name_token out_spot_name_tok
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297 = NCBI:SRA:Illumina:tokenize_spot_name ( _out_name );
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298
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299 NCBI:SRA:spot_name_token in_spot_name_tok
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300 = NCBI:SRA:Illumina:tokenize_spot_name ( NAME );
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301
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302 /* SIGNAL
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303 * optional, no longer archived
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304 */
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305 extern column NCBI:fsamp4 SIGNAL
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306 {
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307 read = out_signal;
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308 validate = < NCBI:fsamp4 > no_compare #1 ( in_signal, out_signal );
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309 }
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310 NCBI:fsamp4 in_signal = SIGNAL;
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311 NCBI:fsamp4 out_signal
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312 = < NCBI:SRA:swapped_fsamp4 > NCBI:SRA:swap ( .SIGNAL, out_x2na_bin );
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313
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314 physical column NCBI:SRA:Illumina:encoding:SIGNAL #2 .SIGNAL
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315 = ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_signal, in_x2na_bin )
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316 | ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_signal, in_2na_bin );
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317
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318 /* NOISE
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319 * optional, no longer archived
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320 */
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321 extern column NCBI:fsamp4 NOISE
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322 {
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323 read = out_noise;
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324 validate = < NCBI:fsamp4 > no_compare #1 ( in_noise, out_noise );
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325 }
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326 NCBI:fsamp4 in_noise = NOISE;
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327 NCBI:fsamp4 out_noise = .NOISE;
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328
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329 physical column NCBI:SRA:Illumina:encoding:NOISE #2 .NOISE = in_noise;
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330
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331 /* INTENSITY
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332 * optional, no longer archived
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333 */
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334 extern column NCBI:fsamp4 INTENSITY
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335 {
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336 read = out_intensity;
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337 validate = < NCBI:fsamp4 > no_compare #1 ( in_intensity, out_intensity );
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338 }
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339 NCBI:fsamp4 in_intensity = INTENSITY;
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340 NCBI:fsamp4 out_intensity
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341 = < NCBI:fsamp4 > NCBI:SRA:denormalize ( out_norm_intensity, out_x2na_bin );
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342 NCBI:fsamp4 out_norm_intensity
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343 = ( NCBI:fsamp4 ) < NCBI:SRA:swapped_fsamp4 > NCBI:SRA:swap ( .INTENSITY, out_x2na_bin );
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344 NCBI:fsamp4 in_norm_intensity
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345 = < NCBI:fsamp4 > NCBI:SRA:normalize ( in_intensity, in_x2na_bin )
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346 | < NCBI:fsamp4 > NCBI:SRA:normalize ( in_intensity, in_2na_bin );
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347 physical column NCBI:SRA:Illumina:encoding:INTENSITY #2 .INTENSITY
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348 = ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_norm_intensity, in_x2na_bin )
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349 | ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_norm_intensity, in_2na_bin );
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350
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351 /* INSDC:tbl:sequence inherited virtual productions
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352 * out_qual_phred
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353 */
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354
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355 /* INSDC:SRA:tbl:spotdesc inherited productions
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356 * static_fixed_spot_len
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357 */
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358 };
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359
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360 /* 4-channel log-odds qualities
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361 *
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362 * history:
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363 * 1.0.2 - updated ancestry
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364 * 1.0.3 - updated ancestry
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365 * 1.0.4 - updated ancestry
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366 * 1.1.0 - updated ancestry
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367 */
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368 table NCBI:SRA:Illumina:tbl:q4:v2 #1.1.0
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369 = NCBI:SRA:Illumina:tbl:v2 #1.0.4
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370 , NCBI:SRA:Illumina:qual4 #2.1.0
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371 {
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372 /* INSDC:SRA:tbl:spotdesc inherited virtual productions
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373 * static_fixed_spot_len
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374 */
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375 };
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376
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377 /* 1-channel log-odds qualities
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378 *
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379 * history:
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380 * 1.0.2 - updated ancestry
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381 * 1.0.3 - updated ancestry
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382 * 1.0.4 - updated ancestry
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383 * 1.1.0 - updated ancestry
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384 */
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385 table NCBI:SRA:Illumina:tbl:q1:v2 #1.1
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386 = NCBI:SRA:Illumina:tbl:v2 #1.0.4
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387 , NCBI:tbl:log_odds_quality #2.1.0
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388 {
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389 /* INSDC:SRA:tbl:spotdesc inherited productions
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390 * static_fixed_spot_len
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391 */
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392 };
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393
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394 /* phred qualities
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395 *
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396 * history:
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397 * 1.0.2 - updated ancestry
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398 * 1.0.3 - updated ancestry
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399 * 1.0.4 - updated ancestry
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400 */
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401 table NCBI:SRA:Illumina:tbl:phred:v2 #1.0.4
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402 = NCBI:SRA:Illumina:tbl:v2 #1.0.4
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403 , NCBI:tbl:phred_quality #2.0.3
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404 {
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405 /* INSDC:SRA:tbl:spotdesc inherited virtual productions
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406 * static_fixed_spot_len
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407 */
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408 };