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, 11:57, 6 April 2010
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| == Read and Validate a SAM/BAM file == | | == Read and Validate a SAM/BAM file == |
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| + | The <code>validate</code> option on the bam executable validates a SAM/BAM file. |
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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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| + | '''NOTE: Currently the only validation that is done is that the file is sorted as specified in the user specified options.''' |
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| === Usage === | | === Usage === |
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| + | ./bam validate --in <inputFile> [--so_flag|--so_unsorted|--so_coord|--so_query] |
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| + | === Return Value === |
| + | * 0: all records are successfully read, are valid, and are properly sorted. |
| + | * non-0: at least one record was not successfully read, not valid, or not properly sorted. |
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| + | === Example Output === |