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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/csra2/read.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 * General read table which will be inherited by others
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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 'insdc/insdc.vschema';
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34 include 'csra2/stats.vschema';
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35
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36
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37 /*--------------------------------------------------------------------------
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38 * tables
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39 */
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40 table NCBI:csra2:tbl:read #1.0 = NCBI:csra2:tbl:read_stats #1
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41 {
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42 /* CHUNK_SZ
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43 * describes the maximum number of bases in any row
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44 *
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45 * if present, allows a single sequence to be broken into multiple rows
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46 * where this value gives the limit on the number of bases in any row.
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47 *
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48 * the sequence will be split across some number of rows, depending upon
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49 * the value of CHUNK_SZ. if length ( seq ) > CHUNK_SZ, then there will
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50 * be multiple rows, where all but the last will have a length of CHUNK_SZ.
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51 * the last ( or only ) row will have a length of length(seq)%CHUNK_SIZE.
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52 */
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53 extern column INSDC:coord:len CHUNK_SZ;
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54
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55
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56 /* READ
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57 * base calls
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58 */
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59
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60 // textual representation
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61 extern default column INSDC:dna:text READ
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62 {
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63 read = out_dna_text;
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64 validate = < INSDC:dna:text > compare ( in_dna_text, out_dna_text );
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65 }
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66
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67 // 4na representation - unpacked
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68 extern column INSDC:4na:bin READ
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69 = out_4na_bin
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70 ;
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71
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72
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73 /* QUALITY
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74 * phred-score quality values
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75 */
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76 extern default column INSDC:quality:phred QUALITY
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77 = out_qual_phred
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78 ;
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79 extern column INSDC:quality:text:phred_33 QUALITY
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80 = ( INSDC:quality:text:phred_33 ) < B8 > sum < 33 > ( out_qual_phred )
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81 ;
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82 extern column INSDC:quality:text:phred_64 QUALITY
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83 = ( INSDC:quality:text:phred_64 ) < B8 > sum < 64 > ( out_qual_phred )
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84 ;
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85
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86 /* ---------------------------- optional columns ---------------------------- */
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87
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88 /* RD_ID
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89 * RD_GROUP
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90 * reports group and id of current row
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91 */
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92 extern column I64 RD_ID;
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93 extern column ascii RD_GROUP;
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94
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95 /* RD_FILTER
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96 * records filter value if used
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97 */
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98 extern column INSDC:SRA:read_filter RD_FILTER;
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99
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100
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101 /* ---------------------------- input rules ---------------------------- */
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102
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103 // input text
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104 INSDC:dna:text in_dna_text
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105 = < INSDC:dna:text, INSDC:dna:text > map < '.acmgrsvtwyhkdbn','NACMGRSVTWYHKDBN' > ( READ )
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106 ;
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107
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108 // input 4na bin
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109 INSDC:4na:bin in_4na_bin
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110 = < INSDC:4na:bin > range_validate < 0, 15 > ( READ )
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111 | < INSDC:dna:text, INSDC:4na:bin > map < INSDC:4na:map:CHARSET, INSDC:4na:map:BINSET > ( in_dna_text )
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112 ;
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113
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114 // input 2na bin
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115 INSDC:2na:bin in_2na_bin
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116 = INSDC:SEQ:rand_4na_2na ( in_4na_bin )
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117 ;
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118
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119 // input 4na alt-read ( ambiguities )
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120 INSDC:4na:bin in_alt_4na_bin
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121 = < INSDC:4na:bin, INSDC:4na:bin > map < INSDC:4na:map:BINSET, [ 15,0,0,3,0,5,6,7,0,9,10,11,12,13,14,15 ] > ( in_4na_bin )
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122 ;
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123
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124 // feed the statistics
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125 INSDC:4na:bin in_stats_seq = in_4na_bin;
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126
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127 // quality
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128 INSDC:quality:text:phred_33 in_qual_text_phred_33 = QUALITY;
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129 INSDC:quality:text:phred_64 in_qual_text_phred_64 = QUALITY;
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130
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131 INSDC:quality:phred in_qual_phred
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132 = QUALITY
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133 | ( INSDC:quality:phred ) < B8 > diff < 33 > ( in_qual_text_phred_33 )
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134 | ( INSDC:quality:phred ) < B8 > diff < 64 > ( in_qual_text_phred_64 )
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135 ;
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136
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137 // feed the statistics
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138 INSDC:quality:phred in_stats_qual_phred = in_qual_phred;
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139
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140 ascii in_stats_read_group
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141 = in_stats_spot_group
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142 | RD_GROUP
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143 ;
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144
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145
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146 /* ---------------------------- physical columns ---------------------------- */
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147
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148 physical column INSDC:2na:packed .READ
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149 = ( INSDC:2na:packed ) pack ( in_2na_bin )
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150 ;
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151
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152 physical column < INSDC:4na:bin > zip_encoding .ALTREAD
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153 = < INSDC:4na:bin > trim < 0, 0 > ( in_alt_4na_bin )
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154 ;
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155
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156 physical column < INSDC:quality:phred > delta_average_zip_encoding .QUALITY
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157 = in_qual_phred
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158 ;
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159
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160
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161 /* ---------------------------- output rules ---------------------------- */
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162
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163 // output 2na packed
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164 INSDC:2na:packed out_2na_packed
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165 = .READ
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166 ;
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167
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168 // output 2na bin
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169 INSDC:2na:bin out_2na_bin
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170 = ( INSDC:2na:bin ) unpack ( out_2na_packed )
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171 ;
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172
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173 // output 2na->4na bin
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174 INSDC:4na:bin out_2na_4na_bin
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175 = < INSDC:2na:bin, INSDC:4na:bin > map < INSDC:2na:map:BINSET, [ 1, 2, 4, 8 ] > ( out_2na_bin )
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176 ;
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177
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178 // output 4na bin
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179 INSDC:4na:bin out_4na_bin
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180 = < INSDC:4na:bin > bit_or < ALIGN_RIGHT > ( out_2na_4na_bin, .ALTREAD )
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181 | out_2na_4na_bin
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182 ;
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183
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184 // output text
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185 INSDC:dna:text out_dna_text
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186 = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_4na_bin )
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187 ;
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188
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189 // output quality
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190 INSDC:quality:phred out_qual_phred
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191 = .QUALITY
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192 | < INSDC:quality:phred > echo < 30 > ( out_4na_bin )
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193 ;
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194 }
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195
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196
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197 /*--------------------------------------------------------------------------
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198 * views
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199 */
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200 table NCBI:csra2:view:read #1.0 =
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201 NCBI:csra2:tbl:read #1.0
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202 {
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203 /* CHUNK_SIZE
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204 * describes the maximum number of bases in any row
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205 *
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206 * if present, allows a single sequence to be broken into multiple rows
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207 * where this value gives the limit on the number of bases in any row.
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208 *
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209 * the sequence will be split across some number of rows, depending upon
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210 * the value of CHUNK_SIZE. if length ( seq ) > CHUNK_SIZE, then there will
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211 * be multiple rows, where all but the last will have a length of CHUNK_SIZE.
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212 * the last ( or only ) row will have a length of length(seq)%CHUNK_SIZE.
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213 */
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214 readonly column INSDC:coord:len CHUNK_SIZE
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215 = .CHUNK_SZ
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216 | < INSDC:coord:len > echo < 0xFFFFFFFF > ()
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217 ;
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218
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219 /* READ
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220 * generate remaining 4 types
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221 */
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222 readonly column INSDC:4na:packed READ
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223 = ( INSDC:4na:packed ) pack ( out_4na_bin )
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224 ;
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225 readonly column INSDC:x2na:bin READ
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226 = < INSDC:4na:bin, INSDC:x2na:bin > map < INSDC:4na:map:BINSET, [ 4,0,1,4,2,4,4,4,3,4,4,4,4,4,4,4 ] > ( out_4na_bin )
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227 ;
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228 readonly column INSDC:2na:bin READ
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229 = out_2na_bin
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230 ;
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231 readonly column INSDC:2na:packed READ
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232 = out_2na_packed
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233 ;
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234
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235 /* READ_ID
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236 * READ_GROUP
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237 * reports group and id of current row
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238 */
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239 readonly column I64 READ_ID
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240 = .RD_ID
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241 | row_id ()
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242 ;
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243 readonly column ascii READ_GROUP
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244 = .RD_GROUP
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245 | < ascii > echo < '' > ()
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246 ;
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247
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248 /* READ_FILTER
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249 * records filter value if used
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250 */
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251 readonly column INSDC:SRA:read_filter READ_FILTER
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252 = .RD_FILTER
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253 | < INSDC:SRA:read_filter > echo < SRA_READ_FILTER_PASS > ()
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254 ;
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255 }