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BamUtil

1,301 bytes added, 17:59, 11 May 2010
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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.
'''NOTE: Currently the only minimal validation that is done is that the file is sorted as specified in the user specified options.'''
=== 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.
--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.
--quitAfterErrorNum : 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.
--maxReportedErrors : Maximum number of errors to print (defaults to 100)
</pre>
=== Usage ===
./bam validate --in <inputFile> [--so_flag|noeof] [--so_unsortedso_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>]
=== Example Output ===
<pre>
The following parameters are in effect:
 
Input Parameters
--in [t.sam], --noeof, --quitAfterErrorNum [-1], --maxReportedErrors [100]
SortOrder : --so_flag, --so_coord, --so_query
 
Record 1
FAIL_PARSE: Too few columns in the Record
 
Record 2
FAIL_PARSE: Too few columns in the Record
 
 
Number of records read = 2
Number of valid records = 0
Returning: 5 (FAIL_PARSE)
</pre>
== Read a SAM/BAM file and write as a SAM/BAM file ==
This executable takes 2 /3 arguments. The first argument is the input file. The second argument is the output file. The executable converts the first file into the format of the second file. So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call:
./bam <bamFile>.bam <newSamFile>.sam
Don't forget to put in the paths to the executable and your test files.
The third argument, <code>NOEOF</code>, specifies that the End-Of-File Block should not be checked for when opening the file.
=== Usage ===
./bam <inputFile> <outputFile.sam/bam/ubam (ubam is uncompressed bam)>[NOEOF] 
=== Return Value ===

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