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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/ncbi.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 Schema intrinsic types and functions
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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
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35
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36 /*--------------------------------------------------------------------------
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37 * data types
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38 */
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39
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40 // N-encoded phred has values limited to 1..63 and 0 used for N
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41 typedef INSDC:quality:phred NCBI:quality:n_encoded:phred;
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42 // N-encoded log-odds has values limite to -5..40 and -6 for N
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43 typedef INSDC:quality:log_odds NCBI:quality:n_encoded:log_odds;
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44
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45 // these types have been restated
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46 alias INSDC:dna:text INSDC:fasta;
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47 alias INSDC:4na:packed INSDC:dna:4na;
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48 alias INSDC:2na:packed INSDC:dna:2na;
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49 alias INSDC:2na:packed NCBI:2na;
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50 alias INSDC:2cs:packed INSDC:color:2cs;
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51 alias INSDC:2cs:packed NCBI:2cs;
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52 alias INSDC:quality:phred NCBI:qual1;
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53 alias NCBI:quality:n_encoded:phred NCBI:SRA:enc_qual1;
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54
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55 // 16-bit integer sample data
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56 typedef I16 NCBI:isamp1;
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57
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58 // 32-bit floating point sample data
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59 typedef F32 NCBI:fsamp1, NCBI:fsamp4 [ 4 ];
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60
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61 // ASN.1
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62 typedef B8 NCBI:asn:binary;
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63 typedef ascii NCBI:asn:text;
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64
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65 // GenInfo id - 64 bit because we are almost out of 32 bit ids
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66 typedef U64 NCBI:gi;
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67
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68 // Taxonomy id
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69 typedef U32 NCBI:taxid;
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70
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71 // Genbank status
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72 typedef U32 NCBI:gb_state;
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73
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74
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75 /*--------------------------------------------------------------------------
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76 * formats
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77 * many of these formats are older than the current corresponding vdb fmts
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78 */
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79
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80 fmtdef merged_t;
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81 fmtdef fp_encoded_t;
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82 fmtdef rl_encoded_t;
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83 fmtdef NCBI:zlib_encoded_t;
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84 fmtdef NCBI:fp_encoded_t;
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85
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86
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87 /*--------------------------------------------------------------------------
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88 * functions
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89 */
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90
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91
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92 /* merge
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93 * split
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94 * the original versions of these functions
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95 * used a slightly different format giving them
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96 * a different signature from their vdb counterparts.
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97 *
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98 * here to maintain backward compatibility for
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99 * column schema functions
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100 */
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101 extern function
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102 merged_t NCBI:merge #1.0 ( any in, ... );
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103
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104 extern function
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105 any NCBI:split #1.0 < U32 idx > ( merged_t in )
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106 = vdb:split;
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107
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108
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109 /* cut
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110 * paste
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111 * these have no compiler type-checking
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112 */
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113 extern function
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114 any NCBI:cut #1.0 < U32 idx, ... > ( any in )
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115 = vdb:cut;
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116
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117 extern function
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118 any NCBI:paste #1.0 ( any in, ... )
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119 = vdb:paste;
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120
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121
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122 /* pack
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123 * unpack
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124 * wildcard typed
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125 */
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126 extern function
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127 any NCBI:pack #1.0 < U32 from, U32 to > ( any in );
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128
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129 extern function
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130 any NCBI:unpack #1.0 < U32 from, U32 to > ( any in );
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131
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132
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133 /* fp_decode
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134 * OBSOLETE
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135 * here to handle anything encoded with fp_encode
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136 */
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137 extern function
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138 any NCBI:fp_decode #1.0 ( fp_encoded_t in );
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139
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140
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141 /* fp_extend
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142 * OBSOLETE
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143 * here to handle anything encoded with fp_truncate
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144 */
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145 extern function
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146 any NCBI:fp_extend #1.0 < U32 bits > ( NCBI:fp_encoded_t in );
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147
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148
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149 /* run_length_encode
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150 * run_length_decode
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151 */
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152 extern function
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153 rl_encoded_t NCBI:run_length_encode #1.0 ( any in )
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154 = vdb:rlencode;
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155
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156 extern function
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157 any NCBI:run_length_decode #1.0 ( rl_encoded_t in )
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158 = vdb:rldecode;
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159
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160
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161 /* zlib
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162 * unzip
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163 * variation on the formatting
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164 */
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165 extern function
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166 NCBI:zlib_encoded_t NCBI:zlib #1.0 < * I32 strategy, I32 level > ( any in )
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167 = vdb:zip;
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168
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169 extern function
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170 any NCBI:unzip #1.0 ( NCBI:zlib_encoded_t in );
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171
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172
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173 /* zlib_huffman_compress
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174 * invokes zlib in huffman + rle mode
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175 */
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176 schema function
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177 NCBI:zlib_encoded_t NCBI:zlib_huffman_compress #1.0 ( any in )
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178 {
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179 // named as Huffman, but apply RLE as well
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180 return NCBI:zlib < Z_RLE > ( in );
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181 }
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182
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183 /* zlib_compress
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184 * standard zlib
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185 */
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186 schema function
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187 NCBI:zlib_encoded_t NCBI:zlib_compress #1.0 ( any in )
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188 {
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189 return NCBI:zlib < Z_DEFAULT_STRATEGY > ( in );
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190 }
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191
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192 /* zlib_decompress
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193 * alternate name for unzip
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194 */
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195 alias NCBI:unzip NCBI:zlib_decompress;