Hello,
When running Picard's 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)
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.