Improved error messages when parameter missing

[jfy133]

It would be useful that the tool does a check for the number of required parameters (those prior to the list of input VCFs), and give a clear error message when not all the expected parameters are provided.

For example, running the following:

$MULTIVCFANALYZER \
NA \
/projects1/calculus_microbiome/evolution/04-analysis/screening/eager/references/${SPECIES^}/*.fa \
/projects1/calculus_microbiome/evolution/04-analysis/screening/eager/references/${SPECIES^}/*.gff \
/projects1/calculus_microbiome/evolution/04-analysis/screening/multivcfanalyzer/output/$PARAM/$SPECIES \
T \
30 \
1 \
0.9 \
0.9 \
${FILES[*]}

where the 'positions to include' parameter is missing, gives the following error:

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3
        at Main.getPositionsToExclude(Main.java:1103)
        at Main.main(Main.java:77)

which for a novice command line/java user would not be clear what the issue would be.