Difference between revisions of "BamUtil"
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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 === | ||
Revision as of 10:57, 6 April 2010
bam Executable
The bam executable has the following functions.
- Read and Validate a SAM/BAM file
- Read a SAM/BAM file and write the same SAM/BAM file.
- Dump a BAM index file into an easy to read text version.
- Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file.
Read and Validate a SAM/BAM file
The validate option on the bam executable 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.
NOTE: Currently the only validation that is done is that the file is sorted as specified in the user specified options.
Usage
./bam validate --in <inputFile> [--so_flag|--so_unsorted|--so_coord|--so_query]
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.
