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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/seq-graph.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 * seq-graph style named annotations
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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
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34
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35 /*--------------------------------------------------------------------------
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36 * types
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37 * constants
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38 */
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39
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40 // example usage of data type:
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41 typedef utf8 NCBI:SeqGraph:sid;
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42 typedef utf8 NCBI:SeqGraph:name;
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43 typedef U32 NCBI:SeqGraph:len;
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44 typedef U32 NCBI:SeqGraph:scale;
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45 typedef I64 NCBI:SeqGraph:value;
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46 typedef NCBI:SeqGraph:value NCBI:SeqGraph:start;
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47 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q0; // min
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48 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q10; // 10th quantile
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49 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q50; // median
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50 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q90; // 90th quantile
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51 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_q100; // max
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52 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q0; // min zoomed to 100bp segment
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53 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q10; // 10th quantile zoomed to 100bp segment
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54 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q50; // median zoomed to 100bp segment
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55 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q90; // 90th quantile zoomed to 100bp segment
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56 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_zoom_q100; // max zoomed to 100bp segment
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57 typedef NCBI:SeqGraph:value NCBI:SeqGraph:gr_num_switches; // number of value switches in graph
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58
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59
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60 /*--------------------------------------------------------------------------
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61 * tables
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62 */
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63 table NCBI:SeqGraph:tbl:seqgraph #1.0
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64 {
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65 /* SID
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66 * Sequence id (Accession.version).
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67 * Indexed.
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68 */
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69 extern column NCBI:SeqGraph:sid SID
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70 = ( NCBI:SeqGraph:sid ) idx:text:project #1.0 < 'sid' > ( .SID );
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71 physical column < NCBI:SeqGraph:sid > zip_encoding .SID
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72 = ( NCBI:SeqGraph:sid ) idx:text:insert #1.0 < 'sid' > ( SID );
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73
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74 /* NAME
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75 * Sequence name (which resolves into SID using assembly information)
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76 * Indexed.
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77 */
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78 extern column NCBI:SeqGraph:name NAME
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79 = ( NCBI:SeqGraph:name ) idx:text:project #1.0 < 'name' > ( .NAME );
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80 physical column < NCBI:SeqGraph:name > zip_encoding .NAME
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81 = ( NCBI:SeqGraph:name ) idx:text:insert #1.0 < 'name' > ( NAME );
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82
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83 /* START
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84 * Sequence offset for the segment saved in this row.
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85 * In most cases this can be calculated from row id and LEN below.
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86 */
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87 extern column < NCBI:SeqGraph:start > izip_encoding START;
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88
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89 /* LEN
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90 * MAX_SEQ_LEN is used in our refseq schema
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91 * CHUNK_SIZE might be preferred
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92 * Mostly a constant ( = 5000), except for the last row for each sequence.
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93 */
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94 extern column < NCBI:SeqGraph:len > izip_encoding LEN;
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95
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96 /* SCALE
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97 * Scaling factor for graph values.
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98 * Mostly needed in order to store values as integers when actual values
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99 * are real with a certain precision.
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100 */
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101 extern column < NCBI:SeqGraph:scale > izip_encoding SCALE;
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102
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103 /* GRAPH
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104 * intensity values
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105 */
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106 extern column < NCBI:SeqGraph:value > izip_encoding GRAPH;
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107
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108
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109 /* GR_Q0
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110 * Minimal value for the row
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111 */
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112 extern column < NCBI:SeqGraph:gr_q0 > izip_encoding GR_Q0;
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113
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114
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115 /* GR_Q10
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116 * 10th quantile value for the row
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117 */
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118 extern column < NCBI:SeqGraph:gr_q10 > izip_encoding GR_Q10;
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119
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120
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121 /* GR_Q50
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122 * Median value for the row
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123 */
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124 extern column < NCBI:SeqGraph:gr_q50 > izip_encoding GR_Q50;
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125
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126
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127 /* GR_Q90
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128 * 90th quantile value for the row
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129 */
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130 extern column < NCBI:SeqGraph:gr_q90 > izip_encoding GR_Q90;
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131
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132
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133 /* GR_Q100
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134 * Maximal value for the row
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135 */
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136 extern column < NCBI:SeqGraph:gr_q100 > izip_encoding GR_Q100;
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137
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138 /* GR_ZOOM_Q0
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139 * Minimal values for 100bp segments of the graph chunk
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140 */
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141 extern column < NCBI:SeqGraph:gr_zoom_q0 > izip_encoding GR_ZOOM_Q0;
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142
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143
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144 /* GR_ZOOM_Q10
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145 * 10th quantile values for 100bp segments of the graph chunk
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146 */
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147 extern column < NCBI:SeqGraph:gr_zoom_q10 > izip_encoding GR_ZOOM_Q10;
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148
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149
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150 /* GR_ZOOM_Q50
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151 * Median values for 100bp segments of the graph chunk
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152 */
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153 extern column < NCBI:SeqGraph:gr_zoom_q50 > izip_encoding GR_ZOOM_Q50;
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154
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155
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156 /* GR_ZOOM_Q90
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157 * 90th quantile values for 100bp segments of the graph chunk
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158 */
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159 extern column < NCBI:SeqGraph:gr_zoom_q90 > izip_encoding GR_ZOOM_Q90;
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160
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161
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162 /* GR_ZOOM_Q100
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163 * Maximal values for 100bp segments of the graph chunk
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164 */
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165 extern column < NCBI:SeqGraph:gr_zoom_q100 > izip_encoding GR_ZOOM_Q100;
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166
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167 /* NUM_SWITCHES
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168 * Number of value switches within the graph. Helps client make the decision how better to
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169 * represent the graph in ASN.1 (Seq-graph or Seq-table).
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170 */
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171 extern column < NCBI:SeqGraph:gr_num_switches > izip_encoding NUM_SWITCHES;
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172 };
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173
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174
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175 database NCBI:SeqGraph:database:kmergraph #1.0
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176 {
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177 table NCBI:SeqGraph:tbl:seqgraph #1.0 LEFT;
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178 table NCBI:SeqGraph:tbl:seqgraph #1.0 RIGHT;
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179 table NCBI:SeqGraph:tbl:seqgraph #1.0 SUM;
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180 }