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| === Parameters === | | === Parameters === |
| <pre> | | <pre> |
− | Required Parameters:
| + | Required Parameters: |
− | --in : the SAM/BAM file to be validated
| + | --in : the SAM/BAM file to be validated |
− | Optional Parameters:
| + | Optional Parameters: |
− | --noeof : do not expect an EOF block on a bam file.
| + | --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_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_coord : validate the file is sorted based on the coordinate. |
− | --so_query : validate the file is sorted based on the query name.
| + | --so_query : validate the file is sorted based on the query name. |
− | --maxErrors : Number of records with errors/invalids to allow before quiting.
| + | --maxErrors : Number of records with errors/invalids to allow before quiting. |
− | -1 (default) indicates to not quit until the entire file is validated.
| + | -1 (default) indicates to not quit until the entire file is validated. |
− | 0 indicates not to read/validate anything.
| + | 0 indicates not to read/validate anything. |
− | --verbose : Print specific error details rather than just a summary
| + | --verbose : Print specific error details rather than just a summary |
− | --printableErrors : Maximum number of records with errors to print the details of
| + | --printableErrors : Maximum number of records with errors to print the details of |
− | before suppressing them when in verbose (defaults to 100)
| + | before suppressing them when in verbose (defaults to 100) |
− | --disableStatistics : Turn off statistic generation
| + | --disableStatistics : Turn off statistic generation |
| + | --params : Print the parameter settings |
| </pre> | | </pre> |
| | | |
| === Usage === | | === Usage === |
| | | |
− | ./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--maxErrors <numErrors>] [--verbose] [--printableErrors <numReportedErrors>] [--disableStatistics] | + | ./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--maxErrors <numErrors>] [--verbose] [--printableErrors <numReportedErrors>] [--disableStatistics] [--params] |
| | | |
| ==== Recommended Usage ==== | | ==== Recommended Usage ==== |
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| ./bam validate --in ~/data/bamExample/37mer_alt.bwa.bam | | ./bam validate --in ~/data/bamExample/37mer_alt.bwa.bam |
| | | |
− | The following parameters are available. Ones with "[]" are in effect:
| |
− |
| |
− | Input Parameters
| |
− | --in [/home/mktrost/data/bamExample/37mer_alt.bwa.bam], --noeof,
| |
− | --maxErrors [-1], --verbose, --printableErrors [100],
| |
− | --disableStatistics
| |
− | SortOrder : --so_flag, --so_coord, --so_query
| |
− |
| |
− | '
| |
| Number of records read = 18900000 | | Number of records read = 18900000 |
| Number of valid records = 18900000 | | Number of valid records = 18900000 |
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| <pre> | | <pre> |
| ./bam validate --in test/testFiles/testInvalid.sam | | ./bam validate --in test/testFiles/testInvalid.sam |
− |
| |
− | The following parameters are available. Ones with "[]" are in effect:
| |
− |
| |
− | Input Parameters
| |
− | --in [test/testFiles/testInvalid.sam], --noeof, --maxErrors [-1], --verbose,
| |
− | --printableErrors [100], --disableStatistics
| |
− | SortOrder : --so_flag, --so_coord, --so_query
| |
− |
| |
| | | |
| Number of records read = 32 | | Number of records read = 32 |
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| <pre> | | <pre> |
| ./bam validate --in test/testFiles/testInvalid.sam --verbose --printableErrors 5 | | ./bam validate --in test/testFiles/testInvalid.sam --verbose --printableErrors 5 |
− |
| |
− | The following parameters are available. Ones with "[]" are in effect:
| |
− |
| |
− | Input Parameters
| |
− | --in [test/testFiles/testInvalid.sam], --noeof, --maxErrors [-1],
| |
− | --verbose [ON], --printableErrors [5], --disableStatistics
| |
− | SortOrder : --so_flag, --so_coord, --so_query
| |
| | | |
| Record 1 | | Record 1 |