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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/align/mate-cache.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 * VDB mate-cache types, functions and tables
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29 */
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30 version 1;
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31
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32 include 'insdc/insdc.vschema';
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33 include 'vdb/vdb.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 * data types
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39 */
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40
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41
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42 /*--------------------------------------------------------------------------
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43 * functions
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44 */
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45
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46
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47 /*--------------------------------------------------------------------------
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48 * tables
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49 */
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50
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51 table NCBI:align:tbl:mate_cache #1.1
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52 {
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53 /* SAM_FLAGS
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54 */
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55 extern column < U32 > izip_encoding SAM_FLAGS_CACHE;
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56
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57 /* SAM_QUALITY
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58 */
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59 extern column < INSDC:quality:text:phred_33 > zip_encoding SAM_QUALITY_CACHE;
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60
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61 /* TEMPLATE_LEN
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62 */
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63 extern column < I32 > izip_encoding TEMPLATE_LEN_CACHE;
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64
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65 /* MATE_ALIGN_ID
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66 */
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67 extern column < I64 > izip_encoding MATE_ALIGN_ID_CACHE;
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68
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69 /* MATE_REF_NAME
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70 */
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71 extern column < ascii > zip_encoding MATE_REF_NAME_CACHE;
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72
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73 /* MATE_REF_POS
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74 */
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75 extern column < INSDC:coord:zero > izip_encoding MATE_REF_POS_CACHE;
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76
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77 /* ALIGNMENT_COUNT
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78 */
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79 extern column < U8 > izip_encoding ALIGNMENT_COUNT_CACHE;
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80
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81 /* RD_FILTER
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82 */
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83 extern column < INSDC:SRA:read_filter > zip_encoding RD_FILTER_CACHE;
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84 readonly column INSDC:SRA:read_filter READ_FILTER_CACHE = .RD_FILTER_CACHE;
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85
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86 /* SPOT_GROUP
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87 */
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88 extern column < ascii > zip_encoding SPOT_GROUP_CACHE;
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89 readonly column ascii SEQ_SPOT_GROUP_CACHE = .SPOT_GROUP_CACHE;
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90 };
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91
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92 /*--------------------------------------------------------------------------
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93 * databases
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94 */
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95
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96 database NCBI:align:db:mate_cache #1
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97 {
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98 table NCBI:align:tbl:mate_cache #1.1 PRIMARY_ALIGNMENT;
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99 };