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=== Parameters ===
=== Parameters ===
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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.
--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
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=== 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 ====
./bam validate --in ~/data/bamExample/37mer_alt.bwa.bam
./bam validate --in ~/data/bamExample/37mer_alt.bwa.bam
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>
./bam validate --in test/testFiles/testInvalid.sam
./bam validate --in test/testFiles/testInvalid.sam
Number of records read = 32
Number of records read = 32
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./bam validate --in test/testFiles/testInvalid.sam --verbose --printableErrors 5
./bam validate --in test/testFiles/testInvalid.sam --verbose --printableErrors 5
Record 1
Record 1
