dangling ends and supplementary alignments

• Thanks to Aleksander Jankowski for fixing the handling of chimeric alignments in hicBuildMatrix (PR #151). Now, for reads with supplementary alignments, only the alignment closer to the 5' end
  of the read is used.

• We discovered that the handling of dangling ends was too strict as all reads starting with the dangling sequence were considered dangling ends (#152). However, a read frequently could start with the dangling sequence but otherwise have a mate from a proper Hi-C re-ligation. Thus, we now only count reads as 'dangling ends' if the mates are within the maximum library insert size distance, face inwards and one of them starts with the dangling sequence.

• As part of this release we also improved the help message of hicBuildMatrix. For this, we replaced the --maxDistance parameter by --maxLibraryInsertSize, which should be based on the measured insert size of the Hi-C library.