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1 .TH tabix 1 "3 February 2015" "htslib-1.2.1" "Bioinformatics tools"
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2 .SH NAME
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3 .PP
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4 bgzip \- Block compression/decompression utility
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5 .PP
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6 tabix \- Generic indexer for TAB-delimited genome position files
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7 .\"
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8 .\" Copyright (C) 2009-2011 Broad Institute.
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9 .\"
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10 .\" Author: Heng Li <lh3@sanger.ac.uk>
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11 .\"
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12 .\" Permission is hereby granted, free of charge, to any person obtaining a
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13 .\" copy of this software and associated documentation files (the "Software"),
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14 .\" to deal in the Software without restriction, including without limitation
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15 .\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
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16 .\" and/or sell copies of the Software, and to permit persons to whom the
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17 .\" Software is furnished to do so, subject to the following conditions:
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18 .\"
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19 .\" The above copyright notice and this permission notice shall be included in
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20 .\" all copies or substantial portions of the Software.
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21 .\"
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22 .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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23 .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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24 .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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25 .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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26 .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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27 .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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28 .\" DEALINGS IN THE SOFTWARE.
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29 .\"
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30 .SH SYNOPSIS
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31 .PP
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32 .B bgzip
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33 .RB [ -cdhB ]
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34 .RB [ -b
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35 .IR virtualOffset ]
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36 .RB [ -s
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37 .IR size ]
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38 .RI [ file ]
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39 .PP
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40 .B tabix
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41 .RB [ -0lf ]
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42 .RB [ -p
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43 gff|bed|sam|vcf]
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44 .RB [ -s
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45 .IR seqCol ]
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46 .RB [ -b
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47 .IR begCol ]
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48 .RB [ -e
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49 .IR endCol ]
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50 .RB [ -S
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51 .IR lineSkip ]
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52 .RB [ -c
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53 .IR metaChar ]
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54 .I in.tab.bgz
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55 .RI [ "region1 " [ "region2 " [ ... "]]]"
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56
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57 .SH DESCRIPTION
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58 .PP
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59 Tabix indexes a TAB-delimited genome position file
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60 .I in.tab.bgz
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61 and creates an index file (
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62 .I in.tab.bgz.tbi
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63 or
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64 .I in.tab.bgz.csi
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65 ) when
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66 .I region
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67 is absent from the command-line. The input data file must be position
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68 sorted and compressed by
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69 .B bgzip
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70 which has a
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71 .BR gzip (1)
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72 like interface. After indexing, tabix is able to quickly retrieve data
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73 lines overlapping
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74 .I regions
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75 specified in the format "chr:beginPos-endPos". Fast data retrieval also
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76 works over network if URI is given as a file name and in this case the
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77 index file will be downloaded if it is not present locally.
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78
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79 .SH INDEXING OPTIONS
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80 .TP 10
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81 .B -0, --zero-based
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82 Specify that the position in the data file is 0-based (e.g. UCSC files)
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83 rather than 1-based.
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84 .TP
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85 .BI "-b, --begin " INT
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86 Column of start chromosomal position. [4]
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87 .TP
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88 .BI "-c, --comment " CHAR
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89 Skip lines started with character CHAR. [#]
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90 .TP
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91 .BI "-C, --csi"
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92 Skip lines started with character CHAR. [#]
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93 .TP
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94 .BI "-e, --end " INT
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95 Column of end chromosomal position. The end column can be the same as the
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96 start column. [5]
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97 .TP
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98 .B "-f, --force "
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99 Force to overwrite the index file if it is present.
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100 .TP
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101 .BI "-m, --min-shift" INT
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102 set minimal interval size for CSI indices to 2^INT [14]
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103 .TP
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104 .BI "-p, --preset " STR
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105 Input format for indexing. Valid values are: gff, bed, sam, vcf.
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106 This option should not be applied together with any of
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107 .BR -s ", " -b ", " -e ", " -c " and " -0 ;
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108 it is not used for data retrieval because this setting is stored in
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109 the index file. [gff]
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110 .TP
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111 .BI "-s, --sequence " INT
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112 Column of sequence name. Option
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113 .BR -s ", " -b ", " -e ", " -S ", " -c " and " -0
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114 are all stored in the index file and thus not used in data retrieval. [1]
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115 .TP
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116 .BI "-S, --skip-lines " INT
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117 Skip first INT lines in the data file. [0]
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118
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119 .SH QUERYING AND OTHER OPTIONS
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120 .TP
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121 .B "-h, --print-header "
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122 Print also the header/meta lines.
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123 .TP
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124 .B "-H, --only-header "
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125 Print only the header/meta lines.
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126 .TP
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127 .B "-i, --file-info "
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128 Print file format info.
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129 .TP
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130 .B "-l, --list-chroms "
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131 List the sequence names stored in the index file.
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132 .TP
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133 .B "-r, --reheader " FILE
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134 Replace the header with the content of FILE
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135 .TP
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136 .B "-R, --regions " FILE
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137 Restrict to regions listed in the FILE. The FILE can be BED file (requires .bed, .bed.gz, .bed.bgz
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138 file name extension) or a TAB-delimited file with CHROM, POS, and, optionally,
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139 POS_TO columns, where positions are 1-based and inclusive. When this option is in use, the input
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140 file may not be sorted.
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141 regions.
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142 .TP
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143 .B "-T, --targets" FILE
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144 Similar to
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145 .B -R
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146 but the entire input will be read sequentially and regions not listed in FILE will be skipped.
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147 .PP
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148 .SH EXAMPLE
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149 (grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
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150
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151 tabix -p gff sorted.gff.gz;
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152
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153 tabix sorted.gff.gz chr1:10,000,000-20,000,000;
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154
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155 .SH NOTES
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156 It is straightforward to achieve overlap queries using the standard
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157 B-tree index (with or without binning) implemented in all SQL databases,
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158 or the R-tree index in PostgreSQL and Oracle. But there are still many
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159 reasons to use tabix. Firstly, tabix directly works with a lot of widely
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160 used TAB-delimited formats such as GFF/GTF and BED. We do not need to
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161 design database schema or specialized binary formats. Data do not need
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162 to be duplicated in different formats, either. Secondly, tabix works on
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163 compressed data files while most SQL databases do not. The GenCode
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164 annotation GTF can be compressed down to 4%. Thirdly, tabix is
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165 fast. The same indexing algorithm is known to work efficiently for an
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166 alignment with a few billion short reads. SQL databases probably cannot
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167 easily handle data at this scale. Last but not the least, tabix supports
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168 remote data retrieval. One can put the data file and the index at an FTP
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169 or HTTP server, and other users or even web services will be able to get
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170 a slice without downloading the entire file.
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171
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172 .SH AUTHOR
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173 .PP
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174 Tabix was written by Heng Li. The BGZF library was originally
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175 implemented by Bob Handsaker and modified by Heng Li for remote file
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176 access and in-memory caching.
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177
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178 .SH SEE ALSO
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179 .PP
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180 .BR samtools (1)
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