updating usage. note that none is now the default

                 [-a about] [-R end] [-S stage] [-p chrom.sizes path]

                 [-y restriction site file] [-z reference genome file]

                 [-C chunk size] [-D Juicer scripts directory]

                 [-Q queue time limit] [-L long queue time limit] [-r] [-h] [-x]

                 [-Q queue time limit] [-L long queue time limit] [-e] [-h] [-x]

* [genomeID] must be defined in the script, e.g. "hg19" or "mm10" (default

  "hg19"); alternatively, it can be defined using the -z command

* [topDir] is the top level directory (default

* [long queue] is the queue for running longer jobs such as the hic file

  creation (default "long")

* [site] must be defined in the script, e.g.  "HindIII" or "MboI"

  (default "MboI")

  (default "none")

* [about]: enter description of experiment, enclosed in single quotes

* -r: use the short read version of the aligner, bwa aln

  (default: long read, bwa mem)

* [end]: use the short read aligner on read end, must be one of 1 or 2

* [stage]: must be one of "merge", "dedup", "final", "postproc", or "early".

* [stage]: must be one of "chimeric", "merge", "dedup", "final", "postproc", or "early".

    -Use "chimeric" when alignments are done but chimeric handling has not finished

    -Use "merge" when alignment has finished but the merged_sort file has not

     yet been created.

    -Use "dedup" when the files have been merged into merged_sort but

  (default 1200)

* [long queue time limit]: time limit for long queue, i.e. -W 168:00 is one week

  (default 3600)

* -x: exclude fragment-delimited maps from hic file creation

* -f: include fragment-delimited maps from hic file creation

* -e: early exit

* -h: print this help and exit

```