Removal of extra input file with coordinates of selected digests

[hansenp]

The class DigestMap was revised and improved. The extra file with coordinates of selected digests that can be passed with the -a option is no longer used, and the information about the state of selection must be passed with the digest file in column 12.

There are some things that need to be done in order to complete this task:

• [x] Remove -a option from command line interface
• [x] Update documentation on read the docs (digest.rst, mapping.rst, count.rst)
• [x] Create GOPHER issue: Enable digest selection via upload of BED file bypassing selection via approaches

[hansenp]

I completely removed the -a option and created an issue for GOPHER:

https://github.com/TheJacksonLaboratory/Gopher/issues/363