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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/csra2/reference.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 * VDB Alignment types, functions and tables
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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 'csra2/stats.vschema';
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34
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35
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36 /*--------------------------------------------------------------------------
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37 * tables
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38 */
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39 table NCBI:csra2:tbl:reference #1.0
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40 = NCBI:csra2:tbl:read_stats #1
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41 {
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42 /* CHUNK_SIZE
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43 * describes the maximum number of bases in any cell
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44 */
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45 extern column INSDC:coord:len CHUNK_SIZE;
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46
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47 /* CIRCULAR
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48 * true if the reference is circular
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49 */
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50 extern column bool CIRCULAR;
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51
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52 /* CANONICAL_NAME
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53 * this should be an accessioned proper name
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54 */
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55 extern column utf8 CANONICAL_NAME;
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56
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57 /* COMMON_NAME
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58 * this name may be ambiguous or missing entirely
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59 */
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60 extern column utf8 COMMON_NAME;
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61
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62 /* LOCAL_SEQUENCE
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63 * supports name overloading by type
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64 */
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65 extern default column INSDC:dna:text LOCAL_SEQUENCE
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66 {
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67 read = out_local_dna_text;
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68 validate = < INSDC:dna:text > compare ( in_local_dna_text, out_local_dna_text );
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69 }
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70 extern column INSDC:4na:bin LOCAL_SEQUENCE = out_local_4na_bin;
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71
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72 /* PRIMARY_ALIGNMENT_IDS
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73 * SECONDARY_ALIGNMENT_IDS
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74 * an index to rows in the PRIMARY_ALIGNMENT and
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75 * SECONDARY_ALIGNMENT tables having alignments
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76 * STARTING within this chunk
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77 *
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78 * the indicies MUST be sorted in clustered order,
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79 * meaning that they are in ascending numeric order
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80 */
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81 extern column < I64 > izip_encoding PRIMARY_ALIGNMENT_IDS;
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82 extern column < I64 > izip_encoding SECONDARY_ALIGNMENT_IDS;
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83
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84 /* OVERLAP_REF_POS
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85 * min ( REF_POS ) for all alignments intersecting this chunk
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86 * but starting in a previous chunk, where the stored position
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87 * is in reference coordinates.
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88 *
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89 * a value of 0 indicates that no alignments starting to
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90 * the left of this chunk also intersect with it.
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91 */
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92 extern column < INSDC:coord:zero > izip_encoding OVERLAP_REF_POS;
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93
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94 /* OVERLAP_REF_LEN
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95 * max ( REF_POS + REF_LEN - CHUNK_START ) % CHUNK_SIZE
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96 * for all alignments intersecting this chunk but starting
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97 * in a previous chunk.
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98 *
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99 * indicates the amount of this chunk that is needed by
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100 * alignments not starting within chunk. so if a slice on
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101 * this reference were to start at 100 bases into this chunk,
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102 * for example, and the OVERLAP_REF_LEN were 100 or less, then
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103 * there are no alignments from prior chunks that need to be
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104 * considered.
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105 */
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106 extern column < INSDC:coord:len > izip_encoding OVERLAP_REF_LEN;
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107
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108 /* COVERAGE
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109 * graphing statistics for the chunk
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110 */
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111
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112 // clipped at 255
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113 extern column < U8 > izip_encoding CGRAPH_HIGH;
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114 extern column < U8 > izip_encoding CGRAPH_LOW;
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115
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116 // count of the number of mismatches in the chunk
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117 extern column < U32 > izip_encoding CGRAPH_MISMATCHES;
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118
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119 // count of the number of inserts and deletes in the chunk
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120 extern column < U32 > izip_encoding CGRAPH_INDELS;
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121
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122
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123 /* writing rules */
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124 INSDC:dna:text in_local_dna_text
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125 = < INSDC:dna:text, INSDC:dna:text > map < '.acmgrsvtwyhkdbn','NACMGRSVTWYHKDBN' > ( LOCAL_SEQUENCE );
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126 ;
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127 INSDC:4na:bin in_local_4na_bin
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128 = < INSDC:4na:bin > range_validate < 0, 15 > ( LOCAL_SEQUENCE )
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129 | < INSDC:dna:text, INSDC:4na:bin > map < INSDC:4na:map:CHARSET, INSDC:4na:map:BINSET > ( in_local_dna_text )
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130 ;
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131 INSDC:2na:bin in_local_2na_bin
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132 = INSDC:SEQ:rand_4na_2na ( in_local_4na_bin )
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133 ;
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134 INSDC:4na:bin in_ambig_4na_bin
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135 = < 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_local_4na_bin );
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136 ;
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137
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138 INSDC:4na:bin in_stats_seq = in_local_4na_bin;
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139
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140 /* physical columns for sequence */
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141 physical column INSDC:2na:packed .LOCAL_SEQUENCE
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142 = ( INSDC:2na:packed ) pack ( in_local_2na_bin )
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143 ;
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144 physical column < INSDC:4na:bin > zip_encoding .LOCAL_AMBIGUITY
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145 = < INSDC:4na:bin > trim < 0, 0 > ( in_ambig_4na_bin )
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146 ;
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147
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148 /* reading rules */
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149 INSDC:2na:packed out_local_2na_packed
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150 = .LOCAL_SEQUENCE
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151 ;
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152 INSDC:2na:bin out_local_2na_bin
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153 = ( INSDC:2na:bin ) unpack ( out_local_2na_packed )
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154 ;
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155 INSDC:4na:bin out_local_2na_4na_bin
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156 = < INSDC:2na:bin, INSDC:4na:bin > map < INSDC:2na:map:BINSET, [ 1, 2, 4, 8 ] > ( out_local_2na_bin );
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157 ;
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158 INSDC:4na:bin out_local_4na_bin
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159 = < INSDC:4na:bin > bit_or < ALIGN_RIGHT > ( out_local_2na_4na_bin, .LOCAL_AMBIGUITY )
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160 ;
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161 INSDC:dna:text out_local_dna_text
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162 = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_local_4na_bin )
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163 ;
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164
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165
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166 INSDC:coord:len in_local_read_len
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167 = ( INSDC:coord:len ) row_len ( in_local_2na_bin )
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168 ;
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169 INSDC:SRA:xread_type in_local_read_type
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170 = < INSDC:SRA:xread_type > echo < SRA_READ_TYPE_BIOLOGICAL > ()
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171 ;
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172 }
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173
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174
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175 /*--------------------------------------------------------------------------
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176 * "views"
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177 */
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178 table NCBI:csra2:view:reference #1.0
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179 = NCBI:csra2:tbl:reference #1.0
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180 {
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181 /* EXTERNAL
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182 * may need to be a function
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183 * it can test the CANONICAL_NAME as in cSRA.v1,
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184 * but if internal it can also check row_length of bases
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185 */
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186 readonly column bool EXTERNAL
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187 = < bool > exists < false > ( .LOCAL_SEQUENCE )
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188 | < bool > echo < true > ()
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189 ;
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190
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191 /* SEQUENCE
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192 * available as text, 4na, x2na, 2na
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193 */
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194 default readonly column INSDC:dna:text SEQUENCE
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195 = out_dna_text
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196 ;
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197 readonly column INSDC:4na:bin SEQUENCE
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198 = out_4na_bin
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199 ;
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200 readonly column INSDC:4na:packed SEQUENCE
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201 = ( INSDC:4na:packed ) pack ( out_4na_bin )
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202 ;
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203 readonly column INSDC:x2na:bin SEQUENCE
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204 = < 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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205 ;
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206 readonly column INSDC:2na:bin SEQUENCE
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207 = out_2na_bin
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208 ;
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209 readonly column INSDC:2na:packed SEQUENCE
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210 = pack ( out_2na_bin )
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211 ;
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212
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213 /* QUALITY
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214 * This is fake column for compatibility
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215 */
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216 readonly column INSDC:quality:phred QUALITY
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217 = out_qual_phred
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218 ;
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219
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220 /* column aliases */
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221 readonly column INSDC:coord:len MAX_SEQ_LEN = .CHUNK_SIZE;
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222 readonly column ascii SEQ_ID = cast ( .CANONICAL_NAME );
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223
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224 /* sequence productions */
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225 INSDC:4na:bin out_4na_bin
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226 = out_local_4na_bin
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227 // TODO: | sub-select from external table
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228 ;
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229
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230 INSDC:dna:text out_dna_text
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231 = < INSDC:4na:bin, INSDC:dna:text > map < INSDC:4na:map:BINSET, INSDC:4na:map:CHARSET > ( out_4na_bin )
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232 ;
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233
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234 INSDC:2na:bin out_2na_bin
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235 = INSDC:SEQ:rand_4na_2na ( out_4na_bin )
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236 ;
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237
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238 /* quality productions */
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239 INSDC:quality:phred out_qual_phred
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240 = < INSDC:quality:phred > echo < 30 > ( SEQUENCE )
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241 ;
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242
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243 INSDC:quality:phred in_stats_qual_phred = out_qual_phred;
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244 }
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245