Docker update for pairtools 1.0*

[agalitsyna]

With this update we:

• [x] Update distiller deendencies
• [x] Update Dockerfile for the most recent pairtools
• [x] Introduce options for dedup

Note that this code uses github version of pairtools and test compiled container galitsyna/distiller_env:0.3.4_dev

Once someone reviews the changes, we can release new pairtools and update the container on dockerhub.