in all pairsamtools, have a unified way to provide/override column indices and the separator

[golobor]

Eg have a flag --col NAME,index that can be repeated multiple types.

[agalitsyna]

@golobor Can you elaborate on this proposal?

1. What's the effect of "flag --col NAME,index", is it similar to re-ordering of columns?
2. The field separator is now taken from _pairsam_format file, and sounds like a reasonable default. Isn't that better you apply a standalone tool for changing the default field separator instead of passing an option for each pairtools module?

Both these questions make me think that we probably need some module for text file manipulations, like picking the columns, checking if their formats comply with the format etc. I guess I was influenced by the discussion about headerops CLI with @Phlya here: #119