About -e $EXCLUDE

[Shaojun Xie]

Could you please give me a short description of -e ?

I'm a little bit of confused.
In the help message:

  *|-e    -c  <STRING>  Comma sep. list of seqids to keep [false].

This means the chrom ID given to -e should be INCLUDEd. But here in the README. you say -e $EXCLUDE.
Which one is correct? Thanks.

[Zev Kronenberg]

For exclusion use -e and for inclusion use -c.

e.g.

-e chrMT,chrY

[Shaojun Xie]

Got it. Thanks.