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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/stats.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 * NCBI Sequence Read Archive schema
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29 */
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30 version 1;
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31
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32 include 'insdc/sra.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 */
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38 typeset NCBI:SRA:stats:qual_type
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39 {
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40 INSDC:quality:phred,
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41 INSDC:quality:log_odds,
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42 INSDC:quality:log_odds [ 4 ]
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43 };
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44
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45
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46 /*--------------------------------------------------------------------------
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47 * functions
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48 */
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49
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50 /*
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51 trigger to build meta statistics: spot count, base count, etc.
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52 */
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53 extern function U8 NCBI:SRA:stats_trigger #1
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54 ( U8 read_bin, U32 read_len, INSDC:SRA:xread_type read_type * ascii spot_group );
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55
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56 /* trigger to build meta statistics from compressed reads
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57 */
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58 extern function
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59 U8 NCBI:SRA:cmp_stats_trigger #1 ( B8 cmp_read_bin, NCBI:SRA:stats:qual_type qual_bin,
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60 U32 read_len, INSDC:SRA:xread_type read_type * ascii spot_group );
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61
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62 extern function
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63 U8 NCBI:SRA:cmpf_stats_trigger #1 ( B8 cmp_read_bin, U32 spot_len,
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64 U32 read_len, INSDC:SRA:xread_type read_type * ascii spot_group );
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65
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66
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67 /* trigger to build phred_quality statistics in meta
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68 */
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69 extern function
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70 U8 NCBI:SRA:phred_stats_trigger #1 ( INSDC:quality:phred qual_bin );
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71
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72 /*--------------------------------------------------------------------------
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73 * table
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74 */
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75
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76 /* stats
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77 * holds sequence statistics
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78 *
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79 * history:
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80 * 1.0.1 - explicitly interit from sra #1.0.1
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81 * 1.1.0 - incorporate stats from compressed read
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82 * 1.1.1 - sra #1.0.2
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83 * 1.1.2 - sra #1.0.3 + cmp_base_count or to base_count
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84 */
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85 table NCBI:SRA:tbl:stats #1.2.0 = INSDC:SRA:tbl:stats #1.1, INSDC:SRA:tbl:sra #1.0.3
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86 {
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87 INSDC:SRA:spotid_t min_spot_id
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88 = < INSDC:SRA:spotid_t > meta:value < "STATS/TABLE/SPOT_MIN" > ();
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89
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90 INSDC:SRA:spotid_t max_spot_id
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91 = < INSDC:SRA:spotid_t > meta:value < "STATS/TABLE/SPOT_MAX" > ();
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92
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93 U64 spot_count
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94 = < U64 > meta:value < "STATS/TABLE/SPOT_COUNT" > ();
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95
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96 U64 base_count
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97 = < U64 > meta:value < "STATS/TABLE/BASE_COUNT" > ();
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98
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99 U64 bio_base_count
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100 = < U64 > meta:value < "STATS/TABLE/BIO_BASE_COUNT" > ();
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101
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102 U64 cmp_base_count
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103 = < U64 > meta:value < "STATS/TABLE/CMP_BASE_COUNT" > () | base_count;
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104
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105 trigger meta_stats
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106 = NCBI:SRA:stats_trigger ( in_stats_bin, in_read_len, in_read_type, in_spot_group )
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107 | NCBI:SRA:stats_trigger ( in_stats_bin, in_read_len, in_read_type )
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108 | NCBI:SRA:cmp_stats_trigger ( in_cmp_stats_bin, in_stats_qual, in_read_len, in_read_type, in_spot_group )
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109 | NCBI:SRA:cmp_stats_trigger ( in_cmp_stats_bin, in_stats_qual, in_read_len, in_read_type )
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110 | NCBI:SRA:cmpf_stats_trigger ( in_cmp_stats_bin, in_spot_len, in_read_len, in_read_type, in_spot_group )
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111 | NCBI:SRA:cmpf_stats_trigger ( in_cmp_stats_bin, in_spot_len, in_read_len, in_read_type );
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112
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113 trigger qual_stats
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114 = NCBI:SRA:phred_stats_trigger #1 ( in_qual_phred );
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115
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116 /* INSDC:SRA:tbl:stats inherited virtual productions
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117 * in_stats_bin
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118 */
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119 };