overlapping prefix adapters · Issue #53 · marcelm/cutadapt (original) (raw)

From marcel.m...@tu-dortmund.de on May 08, 2012 17:27:10

The new -g ^ADAPTER option isn’t enough. There has been a request to allow less strict anchoring, where the adapter overlaps the beginning of the read.

This is easily achieved by this change:
-PREFIX = align.STOP_WITHIN_SEQ2
+PREFIX = align.STOP_WITHIN_SEQ2 | align.START_WITHIN_SEQ1

The question is whether that is the desired behaviour or whether both versions should be possible.

Original issue: http://code.google.com/p/cutadapt/issues/detail?id=43