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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/sra/pevents.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 Likelihood & Event schema
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29 */
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30 version 1;
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31 include 'vdb/vdb.vschema';
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32
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33 typedef U8 INSDC:phred;
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34 typedef ascii INSDC:event:text;
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35 const INSDC:event:text INSDC:event:CHARSET = "ACGT0123B+-";
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36 const INSDC:event:text INSDC:event:ACCEPTSET = "ACGTacgt0123B+-";
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37
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38 extern function < U32 dim >
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39 U32 NCBI:SRA:sort_order #1.0 ( F32[dim] likelihoods );
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40
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41 extern function < U32 dim >
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42 F32 NCBI:SRA:reorder #1.0 ( U32 sort_order, F32[dim] likelihoods );
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43
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44 extern function < U32 dim >
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45 F32 NCBI:SRA:restore_order #1.0 ( U32 sort_order, F32[dim] likelihoods );
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46
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47 extern function < U32 sdim, U32 rdim >
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48 INSDC:phred[rdim] NCBI:SRA:likelihood_to_phred #1.0 ( F32 like_scale, F32[sdim] likelihoods );
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49
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50 extern function < U32 sdim, U32 rdim >
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51 F32[rdim] NCBI:SRA:phred_to_likelihood #1.0 ( F32 like_scale, F32[sdim] phred );
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52
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53 table NCBI:SRA:tbl:pevents #1.0
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54 {
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55 // event labels - single character events
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56 extern column
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57 INSDC:event:text PEVENTS = .PEVENTS;
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58
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59 physical column < INSDC:event:text >
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60 zip_encoding #1.0 .PEVENTS = PEVENTS;
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61
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62 // likelihoods
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63 extern default column
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64 F32[4] LIKELIHOODS = likelihoods;
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65 extern readonly column
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66 INSDC:phred[4] LIKELIHOODS = phred;
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67
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68 U32 sort_encode = NCBI:SRA:sort_order < 4 > ( LIKELIHOODS );
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69
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70 physical column < U32 >
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71 zip_encoding #1.0 < Z_RLE > .SORT_ORDER = sort_encode;
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72
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73 F32 reorder = NCBI:SRA:reorder < 4 > ( sort_encode, LIKELIHOODS );
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74 F32 like_scale = vdb:fixed_vec_sum < F32, 4 > ( reorder );
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75
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76 physical column < F32 >
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77 fzip_encoding #1.0 < 4 > .SCALE = like_scale;
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78
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79 INSDC:phred cut_phred = NCBI:SRA:likelihood_to_phred #1.0 < 4, 3 > ( like_scale, reorder );
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80
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81 physical column < INSDC:phred >
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82 zip_encoding #1.0 < 5 > .PHRED = cut_phred;
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83
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84 // normalization scaling factors
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85 extern readonly column
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86 F32 LIKELIHOOD_NORM = .SCALE;
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87
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88 // phred scores
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89 extern readonly column
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90 INSDC:phred[4] PHRED = phred;
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91 };