SamToFastq should provide an informative error when RG info is missing
See original GitHub issueAs reported in the GATK forum
When running SamToFastq with OUTPUT_PER_RG=T on a bam file without read group information, you get the following error:
Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:148)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:119)
This should be handled to return a more informative error message to the user.
I would guess this should be handled around line 166 of https://github.com/broadinstitute/picard/blob/master/src/java/picard/sam/SamToFastq.java
Issue Analytics
- State:
- Created 7 years ago
- Comments:6 (5 by maintainers)
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Yep, done. Picard doesn’t have nightlies but the source code is public so they can build from source themselves.
Should someone let the user know? I am not sure where this fix is/if Picard has nightlies like GATK?