Suggestion for documentation

[mmterpstra]

This part:

The UMI tag is added as the third field of the read name line. It consists of the molecular barcode extracted from the index read concatenated with the first six bases of R1.

Should be (the bold part is changed):

The UMI tag is added as the third field of the read name line. It consists of the molecular barcode extracted from the index read concatenated with the first six bases of R1 and optionally R2 if present. Then the reads are sorted by umitag.

according to https://github.com/aryeelab/umi/blob/dev/umitag.py#L39

Also the name is a bit misleading of umitag.py because this already preprocesses the file for consolidate.py maybe sortbyumitag.py is more suitable. Or split it in a separate script.