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1 <tool name="ValidateSamFile" id="picard_ValidateSamFile" version="1.122.0">
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2 <description>assess validity of SAM/BAM dataset</description>
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3 <requirements>
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4 <requirement type="package" version="1.122.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11 <command>
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12
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13 ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command
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14
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15 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`
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16
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17 &&
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18
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19 ##set up input files
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20
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21 #set $reference_fasta_filename = "localref.fa"
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22
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23 #if str( $reference_source.reference_source_selector ) == "history":
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24 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
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25 #else:
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26 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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27 #end if
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28
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29 @java_options@
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30
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31 java -jar \$JAVA_JAR_PATH/picard.jar
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32 ValidateSamFile
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33
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34 INPUT="${inputFile}"
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35 OUTPUT="${outFile}"
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36 MODE="${mode}"
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37
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38 #if str( $ignore ) != "None":
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39 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd
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40 IGNORE="${element}"
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41 #end for
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42 #end if
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43
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44 MAX_OUTPUT="${max_output}"
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45 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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46 IGNORE_WARNINGS="${ignore_warnings}"
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47 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
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48 MAX_OPEN_TEMP_FILES=`ulimit -Sn`
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49
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50 VERBOSITY=ERROR
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51 QUIET=true
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52
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53 </command>
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54 <inputs>
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55 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." />
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56 <conditional name="reference_source">
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57 <param name="reference_source_selector" type="select" label="Load reference genome from">
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58 <option value="cached">Local cache</option>
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59 <option value="history">History</option>
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60 </param>
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61 <when value="cached">
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62 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
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63 <options from_data_table="picard_indexes">
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64 <filter type="sort_by" column="2" />
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65 <validator type="no_options" message="No indexes are available" />
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66 </options>
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67 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
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68 </param>
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69 </when>
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70 <when value="history">
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71 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
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72 </when>
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73 </conditional>
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74
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75 <param name="mode" type="select" label="Select output mode" help="MODE">
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76 <option value="VERBOSE">Verbose</option>
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77 <option value="SUMMARY">Summary</option>
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78 </param>
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79 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
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80 <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>
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81 <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>
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82 <option value="INVALID_FLAG_MATE_UNMAPPED"/>
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83 <option value="MISMATCH_FLAG_MATE_UNMAPPED"/>
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84 <option value="INVALID_FLAG_MATE_NEG_STRAND"/>
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85 <option value="MISMATCH_FLAG_MATE_NEG_STRAND"/>
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86 <option value="INVALID_FLAG_FIRST_OF_PAIR"/>
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87 <option value="INVALID_FLAG_SECOND_OF_PAIR"/>
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88 <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND"/>
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89 <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT"/>
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90 <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT"/>
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91 <option value="INVALID_FLAG_READ_UNMAPPED"/>
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92 <option value="INVALID_INSERT_SIZE"/>
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93 <option value="INVALID_MAPPING_QUALITY"/>
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94 <option value="INVALID_CIGAR"/>
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95 <option value="ADJACENT_INDEL_IN_CIGAR"/>
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96 <option value="INVALID_MATE_REF_INDEX"/>
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97 <option value="MISMATCH_MATE_REF_INDEX"/>
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98 <option value="INVALID_REFERENCE_INDEX"/>
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99 <option value="INVALID_ALIGNMENT_START"/>
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100 <option value="MISMATCH_MATE_ALIGNMENT_START"/>
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101 <option value="MATE_FIELD_MISMATCH"/>
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102 <option value="INVALID_TAG_NM"/>
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103 <option value="MISSING_TAG_NM"/>
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104 <option value="MISSING_HEADER"/>
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105 <option value="MISSING_SEQUENCE_DICTIONARY"/>
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106 <option value="MISSING_READ_GROUP"/>
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107 <option value="RECORD_OUT_OF_ORDER"/>
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108 <option value="READ_GROUP_NOT_FOUND"/>
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109 <option value="RECORD_MISSING_READ_GROUP"/>
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110 <option value="INVALID_INDEXING_BIN"/>
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111 <option value="MISSING_VERSION_NUMBER"/>
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112 <option value="INVALID_VERSION_NUMBER"/>
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113 <option value="TRUNCATED_FILE"/>
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114 <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH"/>
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115 <option value="EMPTY_READ"/>
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116 <option value="CIGAR_MAPS_OFF_REFERENCE"/>
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117 <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH"/>
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118 <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH"/>
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119 <option value="E2_BASE_EQUALS_PRIMARY_BASE"/>
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120 <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK"/>
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121 <option value="UNRECOGNIZED_HEADER_TYPE"/>
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122 <option value="POORLY_FORMATTED_HEADER_TAG"/>
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123 <option value="HEADER_TAG_MULTIPLY_DEFINED"/>
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124 <option value="HEADER_RECORD_MISSING_REQUIRED_TAG"/>
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125 <option value="INVALID_DATE_STRING"/>
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126 <option value="TAG_VALUE_TOO_LARGE"/>
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127 <option value="INVALID_INDEX_FILE_POINTER"/>
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128 <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE"/>
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129 <option value="DUPLICATE_READ_GROUP_ID"/>
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130 <option value="MISSING_PLATFORM_VALUE"/>
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131 <option value="INVALID_PLATFORM_VALUE"/>
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132 <option value="DUPLICATE_PROGRAM_GROUP_ID"/>
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133 <option value="MATE_NOT_FOUND"/>
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134 <option value="MATES_ARE_SAME_END"/>
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135 <option value="MISMATCH_MATE_CIGAR_STRING"/>
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136 <option value="MATE_CIGAR_STRING_INVALID_PRESENCE"/>
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137 </param>
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138 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
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139 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
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140 <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/>
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141 <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C->T is not counted as an error in computing the value of the NM tag; default=False"/>
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142
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143 </inputs>
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144
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145 <outputs>
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146 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/>
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147 </outputs>
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148
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149 <tests>
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150 <test>
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151 <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
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152 <param name="reference_source_selector" value="history"/>
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153 <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/>
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154 <param name="mode" value="VERBOSE"/>
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155 <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/>
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156 <param name="max_output" value="100"/>
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157 <param name="ignore_warnings" value="Fasle"/>
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158 <param name="validate_index" value="True"/>
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159 <param name="is_bisulfite_sequenced" value="False"/>
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160 <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
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161 </test>
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162 </tests>
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163
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164 <stdio>
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165 <exit_code range="1:" level="warning"/>
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166 </stdio>
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167
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168 <help>
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169
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170 **Purpose**
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171
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172 Reads a SAM/BAM dataset and report on its validity.
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173
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174 @dataset_collections@
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175
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176 @description@
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177
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178 MODE=Mode
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179 M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the
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180 default value. Possible values: {VERBOSE, SUMMARY}
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181
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182 IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT,
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183 INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED,
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184 INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR,
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185 INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND,
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186 INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT,
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187 INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR,
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188 ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX,
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189 INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START,
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190 MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER,
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191 MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER,
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192 READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN,
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193 MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE,
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194 MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE,
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195 MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH,
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196 E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE,
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197 POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED,
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198 HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE,
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199 INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE,
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200 DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE,
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201 DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END,
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202 MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be
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203 specified 0 or more times.
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204
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205 MAX_OUTPUT=Integer
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206 MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can
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207 be set to 'null' to clear the default value.
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208
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209 REFERENCE_SEQUENCE=File
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210 R=File Reference sequence file, the NM tag check will be skipped if this is missing Default
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211 value: null.
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212
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213 IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can
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214 be set to 'null' to clear the default value. Possible values: {true, false}
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215
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216 VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default
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217 value: true. This option can be set to 'null' to clear the default value. Possible
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218 values: {true, false}
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219
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220 IS_BISULFITE_SEQUENCED=Boolean
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221 BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not
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222 counted as an error in computing the value of the NM tag. Default value: false. This
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223 option can be set to 'null' to clear the default value. Possible values: {true, false}
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224
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225 @more_info@
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226
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227 </help>
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228 </tool>
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229
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230
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