3,045
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0 indicates not to read/validate anything.
0 indicates not to read/validate anything.
--maxReportedErrors : Maximum number of errors to print (defaults to 100)
--maxReportedErrors : Maximum number of errors to print (defaults to 100)
--disableStatistics : Turn off statistic generation
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=== Usage ===
=== Usage ===
./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>]
./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>] [--disableStatistics]
=== Return Value ===
=== Return Value ===
=== Example Output ===
=== Example Output ===
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./bam validate --in t.sam --disableStatistics
The following parameters are in effect:
The following parameters are in effect:
Input Parameters
Input Parameters
--in [t.sam], --noeof, --quitAfterErrorNum [-1], --maxReportedErrors [100]
--in [t.sam], --noeof, --quitAfterErrorNum [-1], --maxReportedErrors [100], --disableStatistics [ON]
SortOrder : --so_flag, --so_coord, --so_query
SortOrder : --so_flag, --so_coord, --so_query
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=== 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 ==
== convert ==
