New development branch & initial commit for zUMIs2.0

## zUMIs.0.0.4

- Added support for plate barcodes with an additional separate barcode fastq file (e.g. for Illumina i7 read)

- Parameters for zUMIs calls are now printed in a '.zUMIs_run.txt' file

## zUMIs.0.0.3

- Implemented up to date Rsubread version

- Introduction of Hamming distance filtering of UMI sequences

- Introduction of binning adjacent cell barcodes by Hamming distance

## zUMIs.0.0.2

- Added inDrops-V3 mode

- Changed output format to sparseMatrix

- Improved adaptive barcode selection

You can find the older version of zUMIs in [zUMIs.0.0.1](https://github.com/sdparekh/zUMIs/releases/tag/zUMIs.0.0.1).

                                 Started job on |	Jul 20 00:44:19

                             Started mapping on |	Jul 20 00:47:11

                                    Finished on |	Jul 20 00:49:29

       Mapping speed, Million of reads per hour |	22.26

                          Number of input reads |	853296

                      Average input read length |	50

                                    UNIQUE READS:

                   Uniquely mapped reads number |	130719

                        Uniquely mapped reads % |	15.32%

                          Average mapped length |	48.41

                       Number of splices: Total |	8929

            Number of splices: Annotated (sjdb) |	4497

                       Number of splices: GT/AG |	8244

                       Number of splices: GC/AG |	185

                       Number of splices: AT/AC |	3

               Number of splices: Non-canonical |	497

                      Mismatch rate per base, % |	5.04%

                         Deletion rate per base |	0.01%

                        Deletion average length |	1.42

                        Insertion rate per base |	0.10%

                       Insertion average length |	2.07

                             MULTI-MAPPING READS:

        Number of reads mapped to multiple loci |	78370

             % of reads mapped to multiple loci |	9.18%

        Number of reads mapped to too many loci |	83

             % of reads mapped to too many loci |	0.01%

                                  UNMAPPED READS:

       % of reads unmapped: too many mismatches |	0.00%

                 % of reads unmapped: too short |	75.43%

                     % of reads unmapped: other |	0.06%

                                  CHIMERIC READS:

                       Number of chimeric reads |	0

                            % of chimeric reads |	0.00%