Demultiplexed a single read with barcodes at both ends

[mvanmoerbeke]

Dear

We are experiencing a particular data setting for which we would like to apply flexbar.
Would it be possible with flexbar to demultiplex reads which have barcodes at both ends, providing a file of barcodes at the start and a file of barcodes at the ends. For example:

BC1: AAATTTGGG
BC2: CCCCCAAAA
Read: AAATTTGGGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCCCCCAAAA

Could this read be demultiplexed to a file called 'out_AAATTTGGG-CCCCCAAAA.fastq' (quite similar as for with the paired read files and the --barcodes2 option but for a single file). Can we use the current version of flexbar for these kind of reads or would this be something that you would consider implementing in one of the next versions?

In addition, I have a small question as well. In the source code, it can be seen that the pairing of files is commented out if paired files are provided. Is there a specific reason to not let flexbar pair a R1 and R2 file, or is this a feature that maybe also can be provided in a next version?

Thank you in advance!

All the best
Marijke