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[[Category:BamUtil|validate]][[Category:BAM Software]][[Category:Software|BamValidator]]== Status ==
The initial version of a SAM/BAM Validator is complete, but does not yet validate all fields or produce all desired statistics. Future releases will add more validation and more statistics.
The BamValidator processes the specified SAM/BAM file:
A valid SAM/BAM file meets the validation criteria specified in [[SAM Validation Criteria]].
Statistics are generated by the BAM Validator if the <code>--disableStatistics</code> option is not set. A description of the statistics generated are found at: [[C++ Class: SamFile#Statistic Generation|Sam File Statistics]]
./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--maxErrors <numErrors>] [--verbose] [--printableErrors <numReportedErrors>] [--disableStatistics] [--params]
If you don't want the file statistics, use --disableStatistics.
./bam validate --in <inputFile> --verbose
= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to be validated
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--refFile : the reference file
--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_query : validate the file is sorted based on the query name.
--maxErrors : Number of records with errors/invalids to allow before quiting.
-1 (default) indicates to not quit until the entire file is validated.
0 indicates not to read/validate anything.
--verbose : Print specific error details rather than just a summary
--printableErrors : Maximum number of records with errors to print the details of
before suppressing them when in verbose (defaults to 100)
--disableStatistics : Turn off statistic generation
--params : Print the parameter settings
</pre>
{{PhoneHomeParamDesc}}
== Required Parameters ==
{{inBAMInputFile|hdr======}}
== Optional Parameters ==
{{noeofBGZFParameter}}
{{refFile}}
=== Validate Sort Order (<code>--so_flag</code>, <code>--so_coord</code>,<code>--so_query</code>)===
Validate the sort order of the file:
* <code>--so_flag</code> - based on the flag in the header
* <code>--so_coord</code> - based on the coordinates/positions
* <code>--so_query</code> - based on the query/read names
=== Print Specific Errors (<code>--maxErrors</code>)===
Use <code>--maxErrors</code> followed by a number to specify the maximum number of records with errors/invalids to process before quiting.
-1 (default) indicates to not quit until the entire file is validated.
0 indicates not to read/validate anything.
=== Print Specific Errors (<code>--verbose</code>)===
Use <code>--verbose</code> to print specific error details rather than just a summary.
=== Maxium Number of Record Error Details to Print (<code>--printableErrors</code>)===Use <code>--printableErrors</code> followed by a number to specify the maximum number of records with errors to print the details of before suppressing them. This parameter is only valid when [[#Print Specific Errors (--verbose)|<code>--verbose</code>]] is also specified. The default is 100. === Disable Statistic Generation (<code>--disableStatistics</code>)===Use <code>--disableStatistics</code> to turn off statistic generation (statistics are generated by default). {{paramsParameter}} {{PhoneHomeParameters}} = Output =The error details (--verbose) and the statistics are printed to stderr. If you want that to go to a file you need to redirect stderr. For a bash shell, redirect to stderr by doing: ./bam validate --in <inputFile> --verbose 2> outputFile.txt = 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.
<pre>
./bam validate --in ~/data/bamExample/37mer_alt.bwa.bam
</pre>
<pre>
./bam validate --in test/testFiles/testInvalid.sam
</pre>
Printable errors is specified to produce a smaller example that does not print all the errors since that would take up more space.
Returning: 7 (INVALID)
</pre>
