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SamToFastq should provide an informative error when RG info is missing

See original GitHub issue

As 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)

Top GitHub Comments

1reaction

vdauweracommented, Mar 20, 2017

Yep, done. Picard doesn’t have nightlies but the source code is public so they can build from source themselves.

0reactions

chandranscommented, Mar 20, 2017

Should someone let the user know? I am not sure where this fix is/if Picard has nightlies like GATK?

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