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java.lang.NullPointerException for Picard SamToFastq OUTPUT_PER_RG=T on bam without read groups
When running Picard's
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)
Obviously the command shouldn't work if there is no read group information, but it would be nice if there was a more informative error provided, as the
NullPointerException makes it seem like an issue with memory allocation.