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2,197 bytes removed, 10:41, 22 July 2010
== validate ==
The <code>validate</code> option on the bam executable reads and validates a SAM/BAM file.  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. SAM fields are validated against: [[SAM Validation Criteria]] '''NOTE: Currently only minimal validation is currently done.''' === Parameters ===<pre> Required Parameters: --in : the SAM/BAM file to be validated Optional Parameters: --noeof : do not expect an EOF block on a bam file. --so_flag : validate the file is sorted based on the header's @HD SO flag. --so_coord : validate the file is sorted based on the coordinate. --so_query : validate the file is sorted based on the query name. --quitAfterErrorNum : Number of records with errors/invalids to allow before quiting. -1 (default) indicates to not quit until the entire file This option is validated. 0 indicates not to read/validate anything. --maxReportedErrors : Maximum number of errors to print (defaults to 100) --disableStatistics : Turn off statistic generation </pre> === Usage ===  ./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>] [--disableStatistics] === Return Value ===* 0: all records are successfully read, are valid, and are properly sorted.* non-0: documented at least one record was not successfully read, not valid, or not properly sorted. === Example Output ===<pre>./bam validate --in t.sam --disableStatistics The following parameters are in effectInput Parameters --in [t.sam], --noeof, --quitAfterErrorNum [-1], --maxReportedErrors [100BamValidator], --disableStatistics [ON] SortOrder : --so_flag, --so_coord, --so_query Record 1FAIL_PARSE: Too few columns in the Record Record 2FAIL_PARSE: Too few columns in the Record  Number of records read = 2Number of valid records = 0Returning: 5 (FAIL_PARSE)</pre> === Statistics Generated ===The following statistics are generated when disableStatistics option is not used:*TotalReads*MappedReads*PairedReads*ProperPair*DuplicateReads*QCFailureReads*MappingRate(%)*PairedReads(%)*ProperPair(%)*DupRate(%)*QCFailRate(%)*TotalBases*BasesInMappedReads
== convert ==

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