Mercurial > repos > charles_s_test > seqsero2

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/clip.vschema @ 3:38ad1130d077 draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
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 'ncbi/sra.vschema';
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33 include 'ncbi/spotname.vschema';
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34
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35
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36 /*--------------------------------------------------------------------------
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37 * NCBI:SRA:tbl:clip
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38 * common clip column processing
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39 * shared by 454 and ion-torrent
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40 *
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41 * uses spotdesc because it has a dependency upon spot_len
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42 *
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43 * history:
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44 * 1.0.1 - base explicitly upon spotdesc #1.0.1
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45 * 1.0.2 - base explicitly upon spotdesc #1.0.2
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46 */
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47 table NCBI:SRA:tbl:clip #1.0.2 = INSDC:SRA:tbl:spotdesc #1.0.2
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48 {
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49 /* CLIP_ADAPTER_LEFT, CLIP_ADAPTER_RIGHT
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50 * adapter clips in 1-based coordinates
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51 * when value is 0, implies that they are NOT SET
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52 */
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53 column INSDC:coord:one CLIP_ADAPTER_LEFT = out_clip_adapt_left;
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54 column INSDC:coord:one CLIP_ADAPTER_RIGHT = out_clip_adapt_right;
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55
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56 // casts are required to allow multple storage formats
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57 INSDC:coord:one out_clip_adapt_left = cast ( .CLIP_ADAPTER_LEFT );
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58 INSDC:coord:one out_clip_adapt_right = cast ( .CLIP_ADAPTER_RIGHT );
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59
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60
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61 /* CLIP_QUALITY_LEFT, CLIP_QUALITY_RIGHT
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62 * quality clips in 1-based coordinates
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63 * when value is 0, implies that they are NOT SET
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64 */
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65 column INSDC:coord:one CLIP_QUALITY_LEFT = out_clip_qual_left;
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66 column INSDC:coord:one CLIP_QUALITY_RIGHT = out_clip_qual_right;
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67
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68 // casts are required to allow multple storage formats
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69 INSDC:coord:one out_clip_qual_left
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70 = cast ( .CLIP_QUALITY_LEFT )
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71 | < INSDC:coord:one > echo < 1 > ();
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72 INSDC:coord:one out_clip_qual_right
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73 = cast ( .CLIP_QUALITY_RIGHT )
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74 | cast ( spot_len );
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75
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76 // support for reading 16-bit clips, as in v1 schema
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77 readonly column U16 CLIP_ADAPTER_LEFT
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78 = .CLIP_ADAPTER_LEFT
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79 | cast ( out_clip_adapt_left );
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80 readonly column U16 CLIP_ADAPTER_RIGHT
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81 = .CLIP_ADAPTER_RIGHT
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82 | cast ( out_clip_adapt_right );
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83 readonly column U16 CLIP_QUALITY_LEFT = cast ( out_clip_qual_left );
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84 readonly column U16 CLIP_QUALITY_RIGHT = cast ( out_clip_qual_right );
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85
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86
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87 /* CLIP-MANIA
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88 */
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89
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90 // 1-based fully-closed right edge is row-length
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91 INSDC:coord:one spot_right = ( INSDC:coord:one ) spot_len;
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92
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93 // processed 1-based coordinates >= 1
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94 INSDC:coord:one lim_clip_adapt_left
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95 = < INSDC:coord:one > clip < 1, 0x7FFFFFFF > ( out_clip_adapt_left );
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96 INSDC:coord:one max_clip_adapt_right
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97 = < INSDC:coord:one, INSDC:coord:one > map < 0, 0x7FFFFFFF > ( out_clip_adapt_right );
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98 INSDC:coord:one lim_clip_adapt_right
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99 = < INSDC:coord:one > min ( spot_right, max_clip_adapt_right );
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100 INSDC:coord:one lim_clip_qual_left
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101 = < INSDC:coord:one > clip < 1, 0x7FFFFFFF > ( out_clip_qual_left );
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102 INSDC:coord:one max_clip_qual_right
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103 = < INSDC:coord:one, INSDC:coord:one > map < 0, 0x7FFFFFFF > ( out_clip_qual_right );
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104 INSDC:coord:one lim_clip_qual_right
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105 = < INSDC:coord:one > min ( spot_right, max_clip_qual_right );
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106
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107 // read-only columns with 0-based coordinates
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108 readonly column INSDC:coord:zero CLIP_ADAPTER_LEFT
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109 = ( INSDC:coord:zero ) < I32 > diff < 1 > ( lim_clip_adapt_left );
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110 readonly column INSDC:coord:zero CLIP_ADAPTER_RIGHT
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111 = ( INSDC:coord:zero ) < I32 > diff < 1 > ( lim_clip_adapt_right );
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112 readonly column INSDC:coord:zero CLIP_QUALITY_LEFT
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113 = ( INSDC:coord:zero ) < I32 > diff < 1 > ( lim_clip_qual_left );
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114 readonly column INSDC:coord:zero CLIP_QUALITY_RIGHT
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115 = ( INSDC:coord:zero ) < I32 > diff < 1 > ( lim_clip_qual_right );
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116
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117 // combined clips
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118 INSDC:coord:one max_clip_left
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119 = < INSDC:coord:one > max ( lim_clip_adapt_left, lim_clip_qual_left )
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120 | lim_clip_adapt_left
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121 | lim_clip_qual_left;
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122 INSDC:coord:zero max_zclip_left
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123 = ( INSDC:coord:zero ) < I32 > diff < 1 > ( max_clip_left );
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124 INSDC:coord:one min_clip_right
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125 = < INSDC:coord:one > min ( lim_clip_adapt_right, lim_clip_qual_right )
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126 | lim_clip_adapt_right
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127 | lim_clip_qual_right;
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128
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129
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130 /* TRIMMED SEQUENCE
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131 * need to find the 0-based trim_start and trim_len
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132 */
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133 INSDC:coord:zero bio_start
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134 = NCBI:SRA:bio_start ( out_read_start, out_read_type );
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135 INSDC:coord:zero trim_start
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136 = < INSDC:coord:zero > max ( bio_start, max_zclip_left )
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137 | bio_start;
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138
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139 INSDC:coord:zero bio_end
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140 = NCBI:SRA:bio_end < false > ( out_read_start, out_read_type, out_read_len );
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141
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142 I32 trim_stop
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143 = < I32 > max ( min_clip_right, trim_start )
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144 | spot_right;
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145 INSDC:coord:len trim_len
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146 = ( INSDC:coord:len ) < I32 > diff ( trim_stop, trim_start );
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147 };