Major changes:

-- Fragment maps no longer included in Hi-C file by default. Before you would exclude them with the -x flag; now use -f to include.
-- dups: now have flag -j for "just exact matches"; this will only eliminate exact match duplicates. Overall this flag is not recommended. However, if you find your jobs are often getting stuck at the dedup phase, it can be because of low complexity or low mapping quality and this flag will allow the jobs to finish much faster. You will still be left with near-duplicates in your library - so use caution when interpreting results. In particular note that near-duplicates are usually machine errors, not true biological results, and thus ought to be removed.
--  Multiple ligation junctions now supported in juicer and statistics.pl script

Minor changes:
- making scripts more consistent by having check for system for juicer_tools path