Convert gene name in upper case

debug rename rules with only prefix

Can load orf and snp effect

Remove output directory from shell execution to avoid directory to be removed when a rerun is called.

added forna controls
deleted varna-3.9.jar

change min-cov works on subject and no more on query.

Add comment in load config file

- do not zip merge_count.cvs
- no more need to have same lib name and fastq file name.

Debug normalization when only 2 libs are provided