What to evaluate should be a mandatory argument

[eudesbarbosa]

Issue
If neither --eval-meis nor --eval-dels is set the script will run without errors and without generating any output.
It is hard to debug.

# Error while running:
Rscript --vanilla /path/to/scramble/cluster_analysis/bin/SCRAMble.R \
            --out-name ...

Suggestions
Either:

1. If neither flag is set, inform user why nothing happened and exit without any other message.
2. Set MEI detection as default behaviour and retire the argument. I'd assume that most people would use the tool for it anyway.

[bioinfo-chru-strasbourg]

+1
When the "_MEIs.txt" is generated, but without any MEIs, the VCF file seems to not be generated :

Done analyzing MEIs
Writing VCF file to /tmp/scramble/sample.vcf...
Error in order(...) : argument 1 is not a vector
Calls: [ ... order -> standardGeneric -> eval -> eval -> eval -> order
Execution halted

Suggestion :
Generate an valid empty VCF