{ts} barcode extract either read

[TomSmithCGAT]

Note, the commits on Jan 24 are from a merge with branch {TS}-EnablePerCellCountTab (PR #308). Probably best to merge that PR before reviewing the changes herein.

See #175 for motivation

• Implements barcode extraction from read1 or read2 with --either-read.
• Implements option to either discard reads where both match, or keep the UMI with highest sequence quality
• Adds test for --either-read

I don't have a good input sample for the test so the current input is hacked together from the indrop data (see tests/README). Basically swapped read1 and read2 at random and use option to identify which read matches the regex. Of course, the output from this is now garbage. I'll post on #175 and ask for more suitable toy data. Also need to add a test to cover --either-read-resolve=quality

[IanSudbery]

I also wonder how hard it would be to allow the user to provide a single regex for both reads.

[TomSmithCGAT]

@IanSudbery - OK for merge?

[IanSudbery]

How about allowing the user to just provide one regex if it can be on either read?

[TomSmithCGAT]

Oops, sorry, missed this!

We could have a single regex option by simply reusing --bc-pattern if --bc-pattern2 is not provided (I assume this is what are thinking).

Personally, I'd rather stick with the current implementation and force the user to be explicit so there's no unexpected behaviour when the regexes are different and they have forgotten to specify --bc-pattern2.

[IanSudbery]

go ahead and merge this.