add --barcode to FastqToBam ?

[bwlang]

right now the docs show:
--platform-unit=String Platform unit (e.g. <flowcell-barcode>.<lane>.<sample-barcode>

I think that does not match with the sam spec:

Platform unit (e.g., flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier.
which does not say anything about sample barcode

Instead I think sample-barcode should go to the BC tag instead, but there is no option for that.

Barcode sequence identifying the sample or library. This value is the expected barcode bases
as read by the sequencing machine in the absence of errors. If there are several barcodes for
the sample/library (e.g., one on each end of the template), the recommended implementation
concatenates all the barcodes separating them with hyphens (‘-’).

Would a PR for that be merged quickly?

[nh13]

The PU (platform-unit) tag need only be a unique identifier. I don't see anything in the code or usage that disagrees with the SAM spec. I don't see anything in the usage that talks about the sample barcode. The example (in parentheses) talks about a flowcell barcode (i.e. a unique string that identifies the flowcell) What am I missing?

We don't have an option to set the BC tag in the read group in SAM header that's true. I'd be ok with a PR for that, and we can get that merged quickly but not sure when a release would be.

[bwlang]

formatting obscured the sample_barcode bit... fixed that just now.
I'll see what I can put together quickly