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, 10:41, 22 July 2010
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| | == validate == | | == validate == |
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| − | The <code>validate</code> option on the bam executable reads and validates a SAM/BAM file. | + | The <code>validate</code> option on the bam executable reads and validates a SAM/BAM file. This option is documented at: [[BamValidator]] |
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| − | The validation checks that the file is sorted as specified in the user options. Default is unsorted, in which case, no order validation is done.
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| − | SAM fields are validated against: [[SAM Validation Criteria]]
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| − | '''NOTE: Currently only minimal validation is currently done.'''
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| − | | |
| − | === Parameters ===
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| − | <pre>
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| − | Required Parameters:
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| − | --in : the SAM/BAM file to be validated
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| − | Optional Parameters:
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| − | --noeof : do not expect an EOF block on a bam file.
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| − | --so_flag : validate the file is sorted based on the header's @HD SO flag.
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| − | --so_coord : validate the file is sorted based on the coordinate.
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| − | --so_query : validate the file is sorted based on the query name.
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| − | --quitAfterErrorNum : Number of records with errors/invalids to allow before quiting.
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| − | -1 (default) indicates to not quit until the entire file is validated.
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| − | 0 indicates not to read/validate anything.
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| − | --maxReportedErrors : Maximum number of errors to print (defaults to 100)
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| − | --disableStatistics : Turn off statistic generation
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| − | </pre>
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| − | | |
| − | === Usage ===
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| − | ./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>] [--disableStatistics]
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| − | | |
| − | === Return Value ===
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| − | * 0: all records are successfully read, are valid, and are properly sorted.
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| − | * non-0: at least one record was not successfully read, not valid, or not properly sorted.
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| − | | |
| − | === Example Output ===
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| − | <pre>
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| − | ./bam validate --in t.sam --disableStatistics
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| − | The following parameters are in effect:
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| − | Input Parameters
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| − | --in [t.sam], --noeof, --quitAfterErrorNum [-1], --maxReportedErrors [100], --disableStatistics [ON]
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| − | SortOrder : --so_flag, --so_coord, --so_query
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| − | Record 1
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| − | FAIL_PARSE: Too few columns in the Record
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| − | Record 2
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| − | FAIL_PARSE: Too few columns in the Record
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| − | Number of records read = 2
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| − | Number of valid records = 0
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| − | Returning: 5 (FAIL_PARSE)
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| − | </pre>
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| − | === Statistics Generated ===
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| − | The following statistics are generated when disableStatistics option is not used:
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| − | *TotalReads
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| − | *MappedReads
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| − | *PairedReads
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| − | *ProperPair
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| − | *DuplicateReads
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| − | *QCFailureReads
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| − | *MappingRate(%)
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| − | *PairedReads(%)
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| − | *ProperPair(%)
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| − | *DupRate(%)
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| − | *QCFailRate(%)
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| − | *TotalBases
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| − | *BasesInMappedReads
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| | == convert == | | == convert == |
