RevertSam does not accept /dev/stdin and should have a better error message
See original GitHub issueHere’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)
Issue Analytics
- State:
- Created 6 years ago
- Comments:6 (4 by maintainers)
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Huh?
On Wed, Dec 6, 2017 at 10:38 AM grozhnev notifications@github.com wrote:
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.