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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/csra2/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 'vdb/vdb.vschema';
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33 include 'insdc/insdc.vschema';
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34 include 'insdc/sra.vschema';
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35
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36
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37 /*--------------------------------------------------------------------------
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38 * functions
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39 */
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40
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41 extern function
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42 U8 NCBI:csra2:stats_trigger #1 ( B8 read_bin * ascii read_group );
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43
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44 extern function
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45 U8 NCBI:csra2:phred_stats_trigger #1 ( INSDC:quality:phred qual_bin )
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46 = NCBI:SRA:phred_stats_trigger;
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47
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48 /*--------------------------------------------------------------------------
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49 * table
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50 */
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51
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52 table NCBI:csra2:tbl:read_stats #1
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53 {
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54 readonly column I64 MIN_READ_ID = min_read_id;
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55 readonly column I64 MAX_READ_ID = max_read_id;
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56 readonly column U64 READ_COUNT = read_count;
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57 readonly column U64 BASE_COUNT = base_count;
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58
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59 /* introduce compatibility names */
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60 readonly column INSDC:SRA:spotid_t MIN_SPOT_ID = cast ( min_read_id );
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61 readonly column INSDC:SRA:spotid_t MAX_SPOT_ID = cast ( max_read_id );
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62 readonly column U64 SPOT_COUNT = read_count;
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63
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64 /* reading rules */
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65 I64 min_read_id
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66 = < I64 > meta:value < "STATS/TABLE/READ_MIN" > ()
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67 | < I64 > meta:value < "STATS/TABLE/SPOT_MIN" > ()
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68 | < I64 > echo < 1 > ()
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69 ;
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70 I64 max_read_id
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71 = < I64 > meta:value < "STATS/TABLE/READ_MAX" > ()
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72 | < I64 > meta:value < "STATS/TABLE/SPOT_MAX" > ()
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73 | cast ( read_count )
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74 ;
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75 U64 read_count
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76 = < U64 > meta:value < "STATS/TABLE/READ_COUNT" > ()
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77 | < U64 > meta:value < "STATS/TABLE/SPOT_COUNT" > ()
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78 ;
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79 U64 base_count
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80 = < U64 > meta:value < "STATS/TABLE/BASE_COUNT" > ()
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81 ;
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82
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83 /* triggers */
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84 trigger meta_stats
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85 = NCBI:csra2:stats_trigger ( in_stats_seq, in_stats_read_group )
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86 | NCBI:csra2:stats_trigger ( in_stats_seq )
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87 ;
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88
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89 trigger qual_stats
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90 = NCBI:csra2:phred_stats_trigger #1 ( in_stats_qual_phred )
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91 ;
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92 }