Iss64 count command

[hansenp]

I finished to transfer the counting of interactions from the subcommand align to the new subcommand count. I structured the command line interface as for the commands truncate and align. Furthermore, I added an extra output file for summary statistics about interactions:

• prefix.count.stats.txt

I also created extensive documentation for the count command on read the docs.

For now, I left the align subcommand untouched. Therefore, there is a lot of redundancy. For instance, the files for interaction interaction counts (and read pair counts at interacting fragments) can now be generated using either align or count, whereby I suffix the corresponding filenames with a 2, if they are generated using the count command:

• prefix.interaction.counts.table.tsv (align)
• prefix.interaction.counts.table2.tsv (count)
• prefix.interacting.fragments.counts.table.tsv (align)
• prefix.interacting.fragments.counts2.table.tsv (count)

For the test data in src/test/resources/data/testInteractionCountsMap/ the contents are identical indicating that the counting of interactions (and read pair counts at interacting fragments) works as before.

If this sanity check is sufficient, we could merge this branch into develop. In a next step we could clean up the align step, which would also involve the simplification of the class ReadPair.