Mercurial > repos > charles_s_test > seqsero2

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/varloc.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 * VarLoc table
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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 'ncbi/ncbi.vschema';
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35
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36
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37 /*--------------------------------------------------------------------------
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38 * types
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39 * http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/asn_spec/Variation-inst.html
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40 */
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41 typedef U8 NCBI:var:inst:type;
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42 const NCBI:var:inst:type NCBI:var:inst:value:unknown = 0;
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43 const NCBI:var:inst:type NCBI:var:inst:value:identity = 1;
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44 const NCBI:var:inst:type NCBI:var:inst:value:inv = 2;
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45 const NCBI:var:inst:type NCBI:var:inst:value:snv = 3;
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46 const NCBI:var:inst:type NCBI:var:inst:value:mnp = 4;
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47 const NCBI:var:inst:type NCBI:var:inst:value:delins = 5;
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48 const NCBI:var:inst:type NCBI:var:inst:value:del = 6;
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49 const NCBI:var:inst:type NCBI:var:inst:value:ins = 7;
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50 const NCBI:var:inst:type NCBI:var:inst:value:microsatellite = 8;
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51 const NCBI:var:inst:type NCBI:var:inst:value:transposon = 9;
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52 const NCBI:var:inst:type NCBI:var:inst:value:cnv = 10;
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53 const NCBI:var:inst:type NCBI:var:inst:value:direct_copy = 11;
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54 const NCBI:var:inst:type NCBI:var:inst:value:rev_direct_copy = 12;
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55 const NCBI:var:inst:type NCBI:var:inst:value:inverted_copy = 13;
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56 const NCBI:var:inst:type NCBI:var:inst:value:everted_copy = 14;
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57 const NCBI:var:inst:type NCBI:var:inst:value:translocation = 15;
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58 const NCBI:var:inst:type NCBI:var:inst:value:prot_missense = 16;
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59 const NCBI:var:inst:type NCBI:var:inst:value:prot_nonsense = 17;
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60 const NCBI:var:inst:type NCBI:var:inst:value:prot_neutral = 18;
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61 const NCBI:var:inst:type NCBI:var:inst:value:prot_silent = 19;
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62 const NCBI:var:inst:type NCBI:var:inst:value:prot_other = 20;
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63 const NCBI:var:inst:type NCBI:var:inst:value:other = 255;
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64
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65 typedef U8 NCBI:var:source:type;
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66 const NCBI:var:source:type NCBI:var:source:value:dbSNP = 1;
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67 const NCBI:var:source:type NCBI:var:source:value:dbVar = 2;
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68 const NCBI:var:source:type NCBI:var:source:value:ClinVar = 3;
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69 const NCBI:var:source:type NCBI:var:source:value:other = 10;
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70
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71
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72 /*--------------------------------------------------------------------------
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73 * functions
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74 */
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75
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76 /* tokenize_var_id
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77 * splits into 2 tokens
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78 * 0 - prefix
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79 * 1 - suffix
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80 */
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81 extern function
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82 text:token NCBI:var:tokenize_var_id #1 ( ascii var_id );
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83
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84
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85 /*--------------------------------------------------------------------------
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86 * varloc
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87 * this name is questionable
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88 */
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89 table NCBI:var:tbl:varloc #1
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90 {
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91 /* SQL schema:
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92 var_id varchar(50),
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93 parent_var_id varchar(50) NULL OKAY,
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94 var_type int,
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95 var_source int,
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96 gi int,
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97 pos_from int,
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98 pos_to int,
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99 entrez_id int,
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100 score int
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101 */
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102
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103 /* VAR_ID
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104 * example: "rs5852452"
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105 */
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106 extern column ascii VAR_ID = out_var_id;
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107
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108 // on input, separate into 3 columns
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109 ascii in_var_id = VAR_ID;
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110 text:token in_var_id_tok = NCBI:var:tokenize_var_id ( in_var_id );
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111 ascii in_var_id_prefix = extract_token < 0 > ( in_var_id, in_var_id_tok );
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112 ascii in_var_id_suffix_text = extract_token < 1 > ( in_var_id, in_var_id_tok );
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113 U32 in_var_id_suffix = strtonum ( in_var_id_suffix_text );
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114
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115 // prefix column
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116 physical column < ascii > zip_encoding .VAR_ID_PREFIX = in_var_id_prefix;
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117 physical column < U32 > izip_encoding .VAR_ID_SUFFIX_LEN = row_len ( in_var_id_suffix_text );
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118 physical column < U32 > izip_encoding .VAR_ID_SUFFIX = in_var_id_suffix;
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119
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120 // on output, restore original id
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121 U32 out_var_id_suffix = .VAR_ID_SUFFIX;
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122 U32 out_var_id_suffix_len = .VAR_ID_SUFFIX_LEN;
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123 ascii out_var_id_prefix = .VAR_ID_PREFIX;
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124 ascii out_var_id = sprintf < "%s%0*u" > ( out_var_id_prefix, out_var_id_suffix_len, out_var_id_suffix );
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125
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126 /* PARENT_VAR_ID
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127 * example: "rs5852452"
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128 * may be EMPTY
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129 */
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130 extern column ascii PARENT_VAR_ID = out_parent_var_id;
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131
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132 // same treatment as VAR_ID
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133 ascii in_parent_var_id = PARENT_VAR_ID;
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134 text:token in_parent_var_id_tok = NCBI:var:tokenize_var_id ( in_parent_var_id );
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135 ascii in_parent_var_id_prefix = extract_token < 0 > ( in_parent_var_id, in_parent_var_id_tok );
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136 ascii in_parent_var_id_suffix_text = extract_token < 1 > ( in_parent_var_id, in_parent_var_id_tok );
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137 U32 in_parent_var_id_suffix = strtonum ( in_parent_var_id_suffix_text );
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138 physical column < ascii > zip_encoding .PARENT_VAR_ID_PREFIX = in_parent_var_id_prefix;
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139 physical column < U32 > izip_encoding .PARENT_VAR_ID_SUFFIX_LEN = row_len ( in_parent_var_id_suffix_text );
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140 physical column < U32 > izip_encoding .PARENT_VAR_ID_SUFFIX = in_parent_var_id_suffix;
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141 U32 out_parent_var_id_suffix = .PARENT_VAR_ID_SUFFIX;
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142 U32 out_parent_var_id_suffix_len = .PARENT_VAR_ID_SUFFIX_LEN;
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143 ascii out_parent_var_id_prefix = .PARENT_VAR_ID_PREFIX;
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144 ascii out_parent_var_id = sprintf < "%s%.*u" > ( out_parent_var_id_prefix, out_parent_var_id_suffix_len, out_parent_var_id_suffix );
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145
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146 /* VAR_TYPE
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147 */
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148 extern column < NCBI:var:inst:type > zip_encoding VAR_TYPE;
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149
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150 /* VAR_SOURCE
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151 */
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152 extern column < NCBI:var:source:type > zip_encoding VAR_SOURCE;
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153
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154 /* GI
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155 */
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156 extern column < NCBI:gi > izip_encoding GI;
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157
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158 /* POS_FROM
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159 * starting position
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160 */
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161 extern column < INSDC:coord:zero > izip_encoding POS_FROM;
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162
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163 INSDC:coord:zero in_pos_from = POS_FROM;
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164 INSDC:coord:zero out_pos_from = .POS_FROM;
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165
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166 /* POS_TO
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167 * ending position
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168 */
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169 extern column INSDC:coord:zero POS_TO = out_pos_to;
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170
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171 INSDC:coord:zero in_pos_to = POS_TO;
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172 INSDC:coord:len in_pos_len = ( INSDC:coord:len ) < I32 > diff < -1 > ( in_pos_to, in_pos_from );
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173
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174 physical column < INSDC:coord:len > izip_encoding .POS_LEN = in_pos_len;
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175
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176 INSDC:coord:zero out_pos_len = ( INSDC:coord:zero ) .POS_LEN;
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177 INSDC:coord:zero out_pos_to = < INSDC:coord:zero > sum < -1 > ( out_pos_from, out_pos_len );
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178
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179 /* ENTREZ_ID
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180 * do we need this?
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181 */
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182 extern column < I32 > izip_encoding ENTREZ_ID;
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183
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184 /* SCORE
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185 */
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186 extern column < I32 > izip_encoding SCORE;
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187 };
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188
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189 table NCBI:var:tbl:hitmap #1
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190 {
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191 extern column U32 MAX_SEQ_LEN; /* must be static */
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192 extern column bool_encoding HITS; /* places on the reference with variations */
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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 * varloc
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198 * contains the varloc table and hit table
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199 */
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200 database NCBI:var:db:varloc #1
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201 {
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202 table NCBI:var:tbl:varloc VARLOC;
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203 table NCBI:var:tbl:hitmap HITMAP;
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204 };