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448 bytes added
, 11:25, 14 July 2010
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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 |
| + | |
| </pre> | | </pre> |
| | | |
| === 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 === |
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| === Example Output === | | === Example Output === |
| <pre> | | <pre> |
| + | ./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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| </pre> | | </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 == | | == convert == |