N in extracted barcode?

[Zhong17]

it seems that whitelist have no N in all the barcodes, but the extracted barcode by proc10X in some reads showed N , and the status tag also show MATHCH. I wonder if it is normal ?

[msettles]

So I suppose in the code an 'N' defaults to an 'A' because of the two bit hashing scheme and so will MATCH when it happens to pair with an A in the whitelist. I've added a check in the lastest commit for any 'N's in the bc seq first and then immediately check for 1-mismatch, which is ok if the N is the only mismatch. So any 'N' in the gem barcode region should not longer "MATCH" a whitelisted barcode, but ok to be MISMATCH1. Needs testing though