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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/align/seq.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 * Sequence 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
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35
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36 /* cmp_base_space
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37 * table representing compressed reads in base space,
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38 * where the bases are only stored for unaligned reads
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39 */
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40 table NCBI:align:tbl:cmp_base_space #1
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41 = INSDC:tbl:sequence #1.0.1
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42 , NCBI:tbl:dcmp_base_space #1
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43 {
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44 /* CMP_READ
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45 * read compressed against a reference sequence
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46 */
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47
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48 // default is IUPAC character representation
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49 extern default column INSDC:dna:text CMP_READ
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50 {
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51 read = out_cmp_dna_text;
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52 validate = < INSDC:dna:text > compare ( in_cmp_dna_text, out_cmp_dna_text );
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53 }
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54
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55 // 4na representation
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56 extern column INSDC:4na:bin CMP_READ = out_cmp_4na_bin;
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57 extern column INSDC:4na:packed CMP_READ = out_cmp_4na_packed;
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58
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59 // x2na representation - 2na with ambiguity
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60 extern column INSDC:x2na:bin CMP_READ = out_cmp_x2na_bin;
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61
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62 // 2na representation - 2na with no ambiguity
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63 extern column INSDC:2na:bin CMP_READ = out_cmp_2na_bin;
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64 extern column INSDC:2na:packed CMP_READ = out_cmp_2na_packed;
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65
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66
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67 /* input processing rules
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68 */
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69
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70 // compressed input text
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71 INSDC:dna:text in_cmp_dna_text
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72 = < INSDC:dna:text, INSDC:dna:text > map < '.acmgrsvtwyhkdbn','NACMGRSVTWYHKDBN' > ( CMP_READ );
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73
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74 // compressed input 4na bin
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75 INSDC:4na:bin in_cmp_4na_bin
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76 = < INSDC:4na:bin > range_validate < 0, 15 > ( CMP_READ )
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77 | ( INSDC:4na:bin ) unpack ( in_cmp_4na_packed )
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78 | < INSDC:dna:text, INSDC:4na:bin > map < INSDC:4na:map:CHARSET, INSDC:4na:map:BINSET > ( in_cmp_dna_text )
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79 | < INSDC:x2na:bin, INSDC:4na:bin > map < INSDC:x2na:map:BINSET, [ 1, 2, 4, 8, 15 ] > ( in_cmp_x2na_bin );
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80
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81 // compressed input 4na packed
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82 INSDC:4na:packed in_cmp_4na_packed = CMP_READ;
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83
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84 // compressed input x2na bin
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85 INSDC:x2na:bin in_cmp_x2na_bin
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86 = < INSDC:x2na:bin > range_validate < 0, 4 > ( CMP_READ )
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87 | < 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 ] > ( in_cmp_4na_bin );
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88
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89 // compressed input 2na bin
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90 INSDC:2na:bin in_cmp_2na_bin
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91 = < INSDC:2na:bin > range_validate < 0, 3 > ( CMP_READ )
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92 | ( INSDC:2na:bin ) unpack ( in_cmp_2na_packed )
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93 | INSDC:SEQ:rand_4na_2na ( in_cmp_4na_bin );
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94
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95 // compressed input 2na packed
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96 INSDC:2na:packed in_cmp_2na_packed = CMP_READ;
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97
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98 // input 4na alt-read ( ambiguities )
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99 INSDC:4na:bin in_cmp_alt_4na_bin
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100 = < 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_cmp_4na_bin );
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101
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102 // preparing a feed into stats column
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103 U8 in_cmp_stats_bin = in_cmp_2na_bin;
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104
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105
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106 /* physical columns
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107 */
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108
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109 physical column INSDC:2na:packed .CMP_READ
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110 = in_cmp_2na_packed
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111 | ( INSDC:2na:packed ) pack ( in_cmp_2na_bin );
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112
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113 physical column < INSDC:4na:bin > zip_encoding .CMP_ALTREAD
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114 = < INSDC:4na:bin > trim < 0, 0 > ( in_cmp_alt_4na_bin );
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115
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116
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117 /* output processing rules
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118 */
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119
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120 // output 2na packed
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121 INSDC:2na:packed out_cmp_2na_packed = .CMP_READ;
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122
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123 // unambiguous unpacked 2na
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124 INSDC:2na:bin out_cmp_2na_bin
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125 = ( INSDC:2na:bin ) unpack ( out_cmp_2na_packed );
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126
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127 // output x2na bin
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128 INSDC:x2na:bin out_cmp_x2na_bin
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129 = < 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_cmp_4na_bin );
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130
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131 // output 2na->4na bin
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132 INSDC:4na:bin out_cmp_2na_4na_bin
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133 = < INSDC:2na:bin, INSDC:4na:bin > map < INSDC:2na:map:BINSET, [ 1, 2, 4, 8 ] > ( out_cmp_2na_bin );
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134
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135 // output 4na bin
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136 INSDC:4na:bin out_cmp_4na_bin
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137 = < INSDC:4na:bin > bit_or < ALIGN_RIGHT > ( out_cmp_2na_4na_bin, .CMP_ALTREAD )
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138 | out_cmp_2na_4na_bin;
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139
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140 // synthesized packed 4na
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141 INSDC:4na:packed out_cmp_4na_packed
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142 = ( INSDC:4na:packed ) pack ( out_cmp_4na_bin );
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143
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144 // output text
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145 INSDC:dna:text out_cmp_dna_text
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146 = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_cmp_4na_bin );
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147
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148
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149 /* decompressed sequences
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150 * source is out_dcmp_4na_bin - a virtual production
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151 */
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152
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153 // synthesize x2na_bin, 2na_bin and 2na_packed
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154 INSDC:x2na:bin out_dcmp_x2na_bin
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155 = < 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_dcmp_4na_bin );
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156 INSDC:2na:bin out_dcmp_2na_bin
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157 = < INSDC:x2na:bin, INSDC:2na:bin > map < [ 0,1,2,3,4 ], [ 0,1,2,3,0 ] > ( out_dcmp_x2na_bin );
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158 INSDC:2na:packed out_dcmp_2na_packed
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159 = ( INSDC:2na:packed ) pack ( out_dcmp_2na_bin );
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160
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161
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162 /* INSDC:tbl:sequence inherited productions
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163 * cs_native
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164 * out_cs_key
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165 * out_signal
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166 * out_2cs_bin
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167 * out_2na_bin
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168 * out_4na_bin
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169 * out_dna_text
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170 * out_x2cs_bin
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171 * out_x2na_bin
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172 * out_2cs_packed
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173 * out_2na_packed
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174 * out_4na_packed
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175 * out_color_text
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176 * out_color_matrix
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177 */
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178
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179 /* NCBI:tbl:dcmp_base_space inherited productions
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180 * out_dcmp_4na_bin
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181 */
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182 }
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183
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184
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185 /* cmp_color_space
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186 * table representing compressed reads in color space,
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187 * where the colors are only stored for unaligned reads
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188 */
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189 table NCBI:align:tbl:cmp_color_space #1 =
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190 INSDC:tbl:sequence #1.0.1, NCBI:tbl:dcmp_color_space #1
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191 {
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192 /* CMP_CSREAD
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193 * read compressed against a reference sequence
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194 */
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195
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196 // default is IUPAC character representation
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197 extern default column INSDC:color:text CMP_CSREAD = out_cmp_color_text;
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198
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199 // x2cs representation - 2cs with ambiguity
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200 extern column INSDC:x2cs:bin CMP_CSREAD = out_cmp_x2cs_bin;
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201
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202 // 2cs representation - 2cs with no ambiguity
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203 extern column INSDC:2cs:bin CMP_CSREAD = out_cmp_2cs_bin;
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204 extern column INSDC:2cs:packed CMP_CSREAD = out_cmp_2cs_packed;
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205
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206
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207 /* input processing rules
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208 */
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209
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210 // compressed input text
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211 INSDC:color:text in_cmp_color_text = CMP_CSREAD;
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212
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213 // compressed input x2cs bin
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214 INSDC:x2cs:bin in_cmp_x2cs_bin
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215 = < INSDC:x2cs:bin > range_validate < 0, 4 > ( CMP_CSREAD )
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216 | < INSDC:color:text, INSDC:x2cs:bin > map < INSDC:x2cs:map:CHARSET, INSDC:x2cs:map:BINSET > ( in_cmp_color_text );
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217
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218 // compressed input 2cs bin
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219 INSDC:2cs:bin in_cmp_2cs_bin
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220 = < INSDC:2cs:bin > range_validate < 0, 3 > ( CMP_CSREAD )
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221 | ( INSDC:2cs:bin ) unpack ( in_cmp_2cs_packed )
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222 | < INSDC:x2cs:bin, INSDC:2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 1, 2, 3, 0 ] > ( in_cmp_x2cs_bin );
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223
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224 // compressed input 2cs packed
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225 INSDC:2cs:packed in_cmp_2cs_packed = CMP_CSREAD;
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226
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227 // compressed input x2cs alt-read ( ambiguities )
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228 INSDC:x2cs:bin in_cmp_alt_x2cs_bin
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229 = < INSDC:x2cs:bin, INSDC:x2cs:bin > map < INSDC:x2cs:map:BINSET, [ 0, 0, 0, 0, 4 ] > ( in_cmp_x2cs_bin );
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230
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231 // preparing a feed into stats column
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232 U8 in_cmp_stats_bin = in_cmp_2cs_bin;
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233
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234
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235 /* physical columns
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236 */
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237
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238 physical column INSDC:2cs:packed .CMP_CSREAD
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239 = in_cmp_2cs_packed
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240 | ( INSDC:2cs:packed ) pack ( in_cmp_2cs_bin );
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241
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242 physical column < INSDC:x2cs:bin > zip_encoding .CMP_ALTCSREAD
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243 = < INSDC:x2cs:bin > trim < 0, 0 > ( in_cmp_alt_x2cs_bin );
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244
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245
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246 /* output processing rules
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247 */
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248
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249 // compressed output 2cs packed
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250 INSDC:2cs:packed out_cmp_2cs_packed = .CMP_CSREAD;
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251
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252 // unambiguous unpacked 2cs
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253 INSDC:2cs:bin out_cmp_2cs_bin
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254 = ( INSDC:2cs:bin ) unpack ( out_cmp_2cs_packed );
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255
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256 // unpacked 2cs with ambiguity
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257 INSDC:x2cs:bin out_cmp_x2cs_bin
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258 = ( INSDC:x2cs:bin ) < U8 > bit_or < ALIGN_RIGHT > ( out_cmp_2cs_bin, .CMP_ALTCSREAD )
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259 | ( INSDC:x2cs:bin ) out_cmp_2cs_bin;
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260
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261 // output text
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262 INSDC:color:text out_cmp_color_text
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263 = < INSDC:x2cs:bin, INSDC:color:text > map < INSDC:x2cs:map:BINSET, INSDC:x2cs:map:CHARSET > ( out_cmp_x2cs_bin );
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264
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265
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266 /* decompressed sequences
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267 * sources are out_dcmp_x2cs_bin - virtual production
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268 */
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269
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270 // synthesize 2cs_bin and 2cs_packed
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271 INSDC:2cs:bin out_dcmp_2cs_bin
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272 = < INSDC:x2cs:bin, INSDC:2cs:bin > map < [ 0,1,2,3,4 ], [ 0,1,2,3,0 ] > ( out_dcmp_x2cs_bin );
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273 INSDC:2cs:packed out_dcmp_2cs_packed
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274 = ( INSDC:2cs:packed ) pack ( out_dcmp_2cs_bin );
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275
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276
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277 /* INSDC:tbl:sequence inherited productions
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278 * cs_native
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279 * out_cs_key
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280 * out_signal
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281 * out_2cs_bin
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282 * out_2na_bin
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283 * out_4na_bin
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284 * out_dna_text
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285 * out_x2cs_bin
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286 * out_x2na_bin
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287 * out_2cs_packed
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288 * out_2na_packed
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289 * out_4na_packed
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290 * out_color_text
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291 * out_qual_phred
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292 * out_color_matrix
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293 * out_qual_text_phred_33
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294 * out_qual_text_phred_64
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295 */
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296
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297 /* NCBI:tbl:dcmp_color_space inherited productions
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298 * out_dcmp_x2cs_bin
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299 */
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300 }