well orientation mod request

[aineniamh]

first use the orientation to assign_bcode_to_well, and then overwrite the coordinates for any sample that have a non-empty coordinate in the well column (if it is there). That would allow you just to (say) swap two samples from the normal order

[aineniamh]

Behaviour:

• If no well specified in barcodes.csv, it will default fill in 1-96 in a vertical orientation, but now actually checks if all 1-96 barcodes have been included in the run. if not, it won't assume they're there. If they're not present, marks the barcodes in those positions as null but still assumes the original orientation.

• If orientation horizontal used, fills in 1-96 row-wise first.

• If a well column specified, it will only show wells that are specified in the barcodes.csv file (see pic)

• The new behaviour will mark wells that aren't in the barcodes.csv as Barcode: "" and the Present/Absent categories as N/A. I think this is more sensible as it doesn't imply all the wells are filled all the time.

• testing the overwriting of some as suggested above resulted in complicated handling cases e.g. what if they specified barcode05 was in well C03, but the default vertical thing would put it in A05- do you mark A05 as empty? do you swap it with something else? do you move all the other wells up one and sub in barcode05? I think less confusing just to say if you supply the wells, you have to supply all the wells you want vizualised.

• Have now added in QC to check the well is in the right format if specified, so that you don't get to the end of the run and realise it's messed up

• Also added QC to check that the well columns specified are unique

• I've also played with the colours and sorted them by what I think is a sensible order in the legend, eg shown below for a run that just has 4 barcodes that someone just chaotically loaded into random wells in a 96-well plate

Examples

Example of running a run with only 4 barcodes specified in the barcodes.csv, but with the specific wells given:

Example of running a default setting (no well specified in barcodes.csv and in vertical orientation) for a run with only barcodes 02, 03, 05 and 07 in the barcodes.csv below: