0.4.0

Added functionality:

• Deduplicating on gene ids ( #44 for motivation):
  The user can now group/dedup according to the gene which the read aligns to. This is useful for single cell RNA-Seq methods such as e.g CEL-Seq where the position of the read on a transcript may be different for reads generated from the same initial molecule. The following options may be used define the gene_id for each read:
  --per-gene
--gene-transcript-map
--gene-tag

• Working with BAM tags (#73, #76, #89):
  UMIs can now be extracted from the BAM tags and_group_ will add a tag to each read describing the read group and UMI. See following options for controlling this behaviour:
  --extract-umi-method
--umi-tag
--umi-group-tag

• Ouput unmapped reads (#78)
  The group command will now output unmapped reads if the --output-unmapped is supplied. These reads will not be assigned to any group.

+ bug fixes for group command (#67, #81) and updated documentation (#77, #79 )