Mercurial > repos > charles_s_test > seqsero2

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/align/pileup-stats.vschema @ 3:38ad1130d077 draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
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 version 1;
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28
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29 include 'vdb/built-in.vschema';
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30 include 'vdb/vdb.vschema';
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31 include 'insdc/insdc.vschema';
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32
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33
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34 /*--------------------------------------------------------------------------
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35 * tables
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36 */
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37
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38 table NCBI:pileup:tbl:pileup_stats #1
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39 {
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40 /* RUN_NAME
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41 * expected to be a single value for entire object
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42 */
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43 extern column ascii RUN_NAME;
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44
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45 /* REFERENCE_SPEC
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46 * the canonical reference accession
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47 * an index is stored in 'ref_spec'.
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48 */
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49 extern column ascii REFERENCE_SPEC = out_reference_spec;
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50 physical < ascii > zip_encoding .REFERENCE_SPEC
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51 = idx:text:insert #1.0 < 'ref_spec' > ( REFERENCE_SPEC );
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52 ascii out_reference_spec
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53 = idx:text:project #1.0 < 'ref_spec' > ( .REFERENCE_SPEC );
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54
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55 /* REF_POS
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56 * we dedicate a row to every position on the reference
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57 * some rows are empty, other than their position
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58 */
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59 extern column I64 REF_POS = out_ref_pos;
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60 physical < I64 > izip_encoding .REF_POS = in_ref_pos;
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61 I64 in_ref_pos
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62 = < I64 > sub_row_id ( REF_POS )
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63 ;
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64 I64 out_ref_pos
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65 = < I64 > add_row_id ( .REF_POS )
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66 | < I64 > add_row_id ( .REF_POS_TRANS )
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67 ;
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68
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69 /* REF_POS_TRANS
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70 * records the translation between current row-id
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71 * and REF_POS, such that
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72 * row-id () + REF_POS_TRANS == REF_POS
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73 */
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74 extern column I64 REF_POS_TRANS = out_ref_pos_trans;
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75 physical < I64 > izip_encoding .REF_POS_TRANS = in_ref_pos_trans;
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76 I64 in_ref_pos_trans
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77 = REF_POS_TRANS
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78 ;
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79 I64 out_ref_pos_trans
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80 = .REF_POS_TRANS
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81 | < I64 > sub_row_id ( .REF_POS )
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82 ;
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83
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84 /* REF_BASE
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85 * this optional column records data extracted from reference
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86 * it is the base at REF_POS
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87 */
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88 extern column < INSDC:dna:text > zip_encoding REF_BASE;
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89
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90 /* DEPTH
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91 * depth of coverage at REF_POS
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92 */
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93 extern column < U32 > izip_encoding DEPTH;
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94
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95 /* MISMATCH_COUNTS
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96 * the number of pileup bases that do not match against REF_BASE
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97 * the normal vector MISMATCH_COUNTS [ 4 ] is recorded as MISMATCH_COUNTS [ 3 ]
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98 * where the element representing REF_BASE has been eliminated.
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99 */
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100 extern column < U32 > izip_encoding MISMATCH_COUNTS;
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101
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102 /* INSERTION_COUNTS
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103 * the number of insertions-before-bases
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104 */
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105 extern column < U32 > izip_encoding INSERTION_COUNTS;
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106
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107 /* DELETION_COUNT
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108 * the number of deletions at REF_POS
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109 */
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110 extern column < U32 > izip_encoding DELETION_COUNT;
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111 }
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112
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113 /*--------------------------------------------------------------------------
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114 * databases
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115 */
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116
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117 database NCBI:pileup:db:pileup_stats #1
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118 {
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119 table NCBI:pileup:tbl:pileup_stats #1 STATS;
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120 }