magicDGS / ReadTools

A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms
https://magicdgs.github.io/ReadTools/
MIT License
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ReadGroupArgumentCollection should not use GATK AddOrReplaceReadGroups args #366

Closed magicDGS closed 6 years ago

magicDGS commented 6 years ago

The ReadGroupArgumentCollection class uses GATK's AddOrReplaceReadGroups 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:

magicDGS commented 6 years ago

Move to pending: I should decide if a port to Picard is worth!

magicDGS commented 6 years ago

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.