Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/join_v17.xml @ 5:64017ce705b6 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit c475b4222a15cdadc6085865f4d13426249fec25-dirty
author yhoogstrate
date Wed, 11 Nov 2015 03:51:05 -0500
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1
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1 <tool id="cg_join" name="Join" version="1.7.1">
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2
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3 <description>Join two tsv files based on equal fields or overlapping regions.</description>
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4
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5 <requirements>
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6 <requirement type="package" version="1">cgatools17</requirement>
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7 </requirements>
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8
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9 <command>
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10 cgatools | head -1;
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11 cgatools join --beta
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12 --input $inputA
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13 --input $inputB
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14 --output $output
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15 --output-mode $outmode
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16 $dump
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17 --select $col
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18 #for $m in $matches
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19 --match ${m.match}
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20 #end for
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21 #if $range_overlap.range == 'yes'
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22 #for $o in $range_overlap.overlaps
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23 --overlap ${o.overlap}
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24 #end for
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25 --overlap-mode $range_overlap.overlapmode
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26 --overlap-fraction-A $range_overlap.fractionA
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27 --boundary-uncertainty-A $range_overlap.boundaryA
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28 --overlap-fraction-B $range_overlap.fractionB
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29 --boundary-uncertainty-B $range_overlap.boundaryB
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30 #end if
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31 </command>
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32
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33
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34 <inputs>
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35 <param name="inputA" type="data" format="tabular" label="Select input file A "/>
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36 <param name="inputB" type="data" format="tabular" label="Select input file B "/>
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37 <param name="col" type="text" value="A.*,B.*" size="40" label="Specify columns for output" help="The default value A.*,B.* prints all columns from both files, other selections enter in the format A.col_name1,A.col_name3,B.col_name1" />
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38
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39 <param name="outmode" type="select" label="Select output mode">
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40 <option value="full" selected="true">full (1 line for each match of records in A and B)</option>
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41 <option value="compact">compact (1 line for each record in A, joining multiple records in B by semicolon)</option>
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42 <option value="compact-pct">compact-pct (same as compact, annotated with % overlap)</option>
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43 </param>
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44
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45 <param name="dump" type="select" label="Select records to print">
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46 <option value="--always-dump" selected="true">print all records of A even if not matched in B</option>
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47 <option value="">print only records of A that are matched in B</option>
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48 </param>
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49
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50 <repeat name="matches" title="Exact match column">
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51 <param name="match" type="text" size="40" label="Enter column:column" help="Enter column_from_A:column_from_B, e.g. chromosome:chromosome"/>
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52 </repeat>
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53
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54 <conditional name="range_overlap">
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55 <param name="range" type="select" label="Do you want to match columns by overlapping range?">
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56 <option value="no">no</option>
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57 <option value="yes">yes</option>
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58 </param>
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59 <when value="no">
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60 <!-- no options -->
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61 </when>
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62 <when value="yes">
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63 <repeat name="overlaps" title="Range column">
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64 <param name="overlap" type="text" size="40" label="Enter column&#91;,column&#93;:column&#91;,column&#93;" help="Enter range_start_from_A&#91;,range_stop_from_A&#93;:range_start_from_B&#91;,range_stop_from_B&#93;, e.g. begin,end:begin,end (overlapping range of positions) or begin,end:position"/>
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65 </repeat>
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66
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67 <param name="overlapmode" type="select" label="Select overlap mode">
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68 <option value="strict" selected="true">strict (overlap if A.begin&lt;B.end and B.begin&gt;A.end)</option>
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69 <option value="allow-abutting-points">allow-abutting-points (overlap if A.begin&lt;B.end and B.begin&gt;A.end, or if A.begin&lt;=B.end and B.begin&lt;=A.end and either A or B has zero length.)</option>
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70 </param>
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71
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72 <param name="fractionA" type="integer" value="0" label="Minimum fraction of A region overlap " />
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73 <param name="boundaryA" type="integer" value="0" label="Boundary uncertainty for A for overlap filtering " help="Records failing the following boundary-uncertainty calculation are not included in the output: overlap length >= overlap-fraction-A * (A-range-length - boundary-uncertainty-A)"/>
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74
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75 <param name="fractionB" type="integer" value="0" label="Minimum fraction of B region overlap " />
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76 <param name="boundaryB" type="integer" value="0" label="Boundary uncertainty for overlap filtering " help="Records failing the following boundary-uncertainty calculation are not included in the output: overlap length >= overlap-fraction-B * (B-range-length - boundary-uncertainty-B)"/>
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77 </when>
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78 </conditional>
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79
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80 <!-- prefix for output file so you dont have to manually rename history items -->
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81 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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82
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83 </inputs>
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84
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85 <outputs>
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86 <data format="tabular" name="output" label="$fname ${tool.name} on data ${on_string}" />
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87 </outputs>
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88
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89
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90 <help>
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91
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92 **What it does**
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93
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94 This tool joins two tab-delimited files based on equal fields or overlapping regions.
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95
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96 **cgatools 1.7.1 Documentation**
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97
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98 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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99
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100 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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101
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102 **Command line reference**::
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103
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104 COMMAND NAME
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105 join - Joins two tab-delimited files based on equal fields or overlapping regions.
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106
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107 DESCRIPTION
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108 Joins two tab-delimited files based on equal fields or overlapping regions.
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109 By default, an output record is produced for each match found between file
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110 A and file B, but output format can be controlled by the --output-mode
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111 parameter.
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112
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113 OPTIONS
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114 -h [ --help ]
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115 Print this help message.
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116
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117 --beta
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118 This is a beta command. To run this command, you must pass the --beta
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119 flag.
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120
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121 --input arg
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122 File name to use as input (may be passed in as arguments at the end of
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123 the command), or omitted for stdin). There must be exactly two input
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124 files to join. If only one file is specified by name, file A is taken
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125 to be stdin and file B is the named file. File B is read fully into
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126 memory, and file A is streamed. File A's columns appear first in the
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127 output.
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128
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129 --output arg (=STDOUT)
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130 The output file name (may be omitted for stdout).
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131
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132 --match arg
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133 A match specification, which is a column from A and a column from B
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134 separated by a colon.
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135
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136 --overlap arg
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137 Overlap specification. An overlap specification consists of a range
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138 definition for files A and B, separated by a colon. A range definition
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139 may be two columns, in which case they are interpreted as the beginning
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140 and end of the range. Or it may be one column, in which case the range
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141 is defined as the 1-base range starting at the given value. The records
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142 from the two files must overlap in order to be considered for output.
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143 Two ranges are considered to overlap if the overlap is at least one
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144 base long, or if one of the ranges is length 0 and the ranges overlap
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145 or abut. For example, "begin,end:offset" will match wherever end-begin
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146 &gt; 0, begin&lt;offset+1, and end&gt;offset, or wherever end-begin = 0,
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147 begin&lt;=offset+1, and end&gt;=offset.
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148
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149
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150 -m [ --output-mode ] arg (=full)
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151 Output mode, one of the following:
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152 full Print an output record for each match found between
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153 file A and file B.
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154 compact Print at most one record for each record of file A,
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155 joining the file B values by a semicolon and
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156 suppressing repeated B values and empty B values.
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157 compact-pct Same as compact, but for each distinct B value,
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158 annotate with the percentage of the A record that is
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159 overlapped by B records with that B value. Percentage
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160 is rounded up to nearest integer.
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161
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162 --overlap-mode arg (=strict)
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163 Overlap mode, one of the following:
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164 strict Range A and B overlap if A.begin &lt; B.end and
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165 B.begin &lt; A.end.
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166 allow-abutting-points Range A and B overlap they meet the strict
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167 requirements, or if A.begin &lt;= B.end and
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168 B.begin &lt;= A.end and either A or B has zero
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169 length.
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170
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171 --select arg (=A.*,B.*)
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172 Set of fields to select for output.
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173
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174 -a [ --always-dump ]
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175 Dump every record of A, even if there are no matches with file B.
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176
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177 --overlap-fraction-A arg (=0)
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178 Minimum fraction of A region overlap for filtering output.
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179
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180 --boundary-uncertainty-A arg (=0)
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181 Boundary uncertainty for overlap filtering. Specifically, records
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182 failing the following predicate are filtered away: overlap &gt;=
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183 overlap-fraction-A * ( A-range-length - boundary-uncertainty-A )
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184
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185 --overlap-fraction-B arg (=0)
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186 Minimum fraction of B region overlap for filtering output.
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187
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188 --boundary-uncertainty-B arg (=0)
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189 Boundary uncertainty for overlap filtering. Specifically, records
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190 failing the following predicate are filtered away: overlap &gt;=
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191 overlap-fraction-B * ( B-range-length - boundary-uncertainty-B )
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192
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193 SUPPORTED FORMAT_VERSION
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194 Any
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195 </help>
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196 </tool>