RevertSam does not accept /dev/stdin and should have a better error message

Here’s the cryptic error message when we try and run RevertSam with I=/dev/stdin. Full command line:

RevertSam INPUT=/dev/stdin OUTPUT=/dev/stdout SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=false REMOVE_DUPLICATE_INFORMATION=false REMOVE_ALIGNMENT_INFORMATION=false ATTRIBUTE_TO_CLEAR=[] SANITIZE=true

Stack trace:

Exception in thread "main" htsjdk.samtools.SAMException: Cannot determine candidate qualities: no qualities found.
	at htsjdk.samtools.util.QualityEncodingDetector.generateCandidateQualities(QualityEncodingDetector.java:228)
	at htsjdk.samtools.util.QualityEncodingDetector.generateBestGuess(QualityEncodingDetector.java:382)
	at htsjdk.samtools.util.QualityEncodingDetector.detect(QualityEncodingDetector.java:335)
	at picard.sam.RevertSam.createReadGroupFormatMap(RevertSam.java:534)
	at picard.sam.RevertSam.doWork(RevertSam.java:271)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:96)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:106)

[yfarjoun]

Huh?

On Wed, Dec 6, 2017 at 10:38 AM grozhnev [e-mail] wrote:

As it is clear to me, you got the exception because of SANITIZE=true. What is the purpose of using this parameter? In the documentation RevertSam http://broadinstitute.github.io/picard/command-line-overview.html#RevertSam it is said that

SANITIZE (Boolean) WARNING: This option is potentially destructive. If enabled will discard reads in order to produce a consistent output BAM. Reads discarded include (but are not limited to) paired reads with missing mates, duplicated records, records with mismatches in length of bases and qualities. This option can only be enabled if the output sort order is queryname and will always cause sorting to occur. Default value: false. This option can be set to ‘null’ to clear the default value. Possible values: {true, false}

So, if it is not necessary, it is better not to use it.

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[sooheelee]

A researcher has reported on the forum that the streaming error depends on the parameter SANITIZE=true at https://gatkforums.broadinstitute.org/gatk/discussion/comment/49098#Comment_49098 and also thinks it odd that if the end point of a stream is ReverSam that this should then error the tool.