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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/align/qstat.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 Quality Statistics 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 'ncbi/ncbi.vschema';
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34
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35 table NCBI:align:tbl:qstat #1.0
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36 {
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37 /* SPOT_GROUP
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38 */
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39 extern column < ascii > zip_encoding SPOT_GROUP;
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40
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41 /* CYCLE
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42 * machine cycle
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43 */
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44 extern column < U32 > izip_encoding CYCLE;
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45
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46 /* KMER
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47 * use dimer
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48 */
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49 extern column INSDC:dna:text KMER;
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50
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51 /* HPRUN
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52 * homopolymer run
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53 * number of bases of the same type preceding the current base
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54 */
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55 extern column < INSDC:coord:len > izip_encoding HPRUN;
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56
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57 /* GC_CONTENT
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58 * number of G's or C's in the 7 bases preceding the current base
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59 */
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60 extern column < U32 > izip_encoding GC_CONTENT;
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61
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62 /* ORIG_QUAL
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63 * original quality scores
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64 */
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65 extern column < INSDC:quality:phred > zip_encoding ORIG_QUAL;
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66
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67 /* MAX_QUAL
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68 * max. quality score in read
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69 */
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70 extern column < INSDC:quality:phred > zip_encoding MAX_QUAL;
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71
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72 /* NREAD
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73 * number of the read
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74 */
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75 extern column < U8 > zip_encoding NREAD;
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76
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77 /* TOTAL_COUNT
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78 * total count of observed events
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79 */
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80 extern column < U32 > izip_encoding TOTAL_COUNT;
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81
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82 /* MISMATCH_COUNT
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83 * count of observed mismatches
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84 */
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85 extern column < U32 > izip_encoding MISMATCH_COUNT;
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86
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87 };