Hicstuff

Add feature to filter pcr duplicates:

* Can be enabled with the `-D` / `--duplicates` flag in the command `hicstuff pipeline`.
* python function `filter_pcr_dup` in pipeline.py can be used directly on a pairs file.

:warning: Intoduces non-backwards compatible changes to the CLI:
* Option `-m, --minimap2` becomes `-a, --aligner`, taking either "minimap2" or "bowtie2" as value
* Option `-f, --fasta` becomes `-g, --genome`

Changes in behaviour:
* `-g` must be a fasta file when using minimap2, and a bowtie2 index prefix when using bowtie2
* A fasta file is created among temporary file when using bowtie2. It is generated from the bt2 index.