marcelm/cutadapt — pull request #1 by jamescasbon (2012-06-29 14:08:30+00:00)
Title: Add --discard-untrimmed and basic paired end support

My use case is that I want to keep a paired end file in sync (i.e. with exacylt the same number and read accessions) while discarding those reads that did not trim. This supports that behaviour.

It has tests.