Include barcode frequency report among those generated during demux

[tomkinsc]

A new sub-command, common_barcodes, has been added to viral-ngs/illumina.py. This command writes a report listing the barcodes present in a sequencer run, sorted by frequency in descending order. The information is helpful for troubleshooting whether or not a barcode may have been entered incorrectly in the original sample sheet.

This command will be available in the next release of viral-ngs.

It would be helpful to add a call to this command to the demultiplexing applet, so the barcode report is among those generated by that step.

[tomkinsc]

This has been refactored a bit. While the aforementioned command still exists, the same report can now be created by specifying the --commonBarcodes argument to illumina_demux (it's the path of the file to write with the barcode counts).

[yifei-men]

Thanks @tomkinsc for the headsup

Note to self: Update resource tarball to next tag release.. 1.5.6 (?) and test with --commonBarcodes <barcode_report_fn> argument

[yifei-men]

Note to self: function included in upstream v1.6.0 release

[yifei-men]

Addressed by #30