Closed magicDGS closed 6 years ago
Move to pending: I should decide if a port to Picard is worth!
After all the problems that using arguments from Picard/GATK in our toolkit, I decided to do not go in this direction anymore. It is true that GATK was a pre-release when I was using it for ReadTools, but still it might be problematic at some point. Maybe I will come back to the idea later.
The
ReadGroupArgumentCollection
class uses GATK'sAddOrReplaceReadGroups
arguments, but this was a port of a picard tool which was removed when GATK changed to import the picard project instead. To update GATK to the 4.0.0.0 release, we should:AddOrReplaceReadGroups
for the argument names to picardAddOrReplaceReadGroups
arguments from picard in our code.