Increase flexibility in adapters trimming?

[jkh00]

Hi,

Would it be possible to include options such as:

1. Disable splitting (ignore middle adapters?)
2. Discard reads containing middle adapters

Splitting reads will mess up with the methylation (MM/ML) tags of the reads, as this information will not be carried over properly. Therefore, having these parameters would be especially useful for those working on methylation data.

Many thanks in advance!
Jin