After #442, we will include a GATK-patched version specific for ReadTools from the bioinformagik fork (https://github.com/bioinformagik/gatk), but I would like to move to a maven dependency to be able to move forward in the development without extra work.
To do so, we should move to ReadTools v.2.0.0, because the command-line will change. This requires a lot of other work and should be planned in the near future.
After #442, we will include a GATK-patched version specific for ReadTools from the bioinformagik fork (https://github.com/bioinformagik/gatk), but I would like to move to a maven dependency to be able to move forward in the development without extra work.
To do so, we should move to ReadTools v.2.0.0, because the command-line will change. This requires a lot of other work and should be planned in the near future.