Search for adapter at 5' end only

[GoogleCodeExporter]

Under some circumstances it makes sense to allow the adapter to only occur in 
the 5' end of a read.

Original issue reported on code.google.com by marcel.m...@tu-dortmund.de on 29 Jun 2011 at 8:38

[GoogleCodeExporter]

I would like this behaviour, I have attached an initial patch.

It enforces that the read actually starts with the adaptor - which is different 
behaviour to the 3' trim which can allow a match.

Original comment by cas...@gmail.com on 1 Oct 2011 at 7:22

Attachments:

• 0001-initial-work-on-5-prime-mode.patch

[GoogleCodeExporter]

Thanks a lot, this is really great! I've started to review and integrate the 
patch, but I'm uncertain as to how the behavior should be in case the adapter 
is found within the read. With your patch, such a match would be ignored, but I 
have a report from another user who would like to get the adapter and the 
preceding bases trimmed.

Both variants could be implemented of course, but that would add two more 
command-line parameters of which there are quite a few already. Could you tell 
me why it makes sense to ignore these matches within reads?

Original comment by marcel.m...@tu-dortmund.de on 31 Oct 2011 at 11:13

[GoogleCodeExporter]

Yes, having the adaptor with the preceeding bases trimmed would be ideal. 

I think when I wrote the patch, the assumption that the trimming would be at 
the back was quite integral to the code.  However, a bigger patch could 
probably do it better.

Original comment by cas...@gmail.com on 31 Oct 2011 at 6:11

[GoogleCodeExporter]

An updated version of your patch has been integrated into cutadapt in r214 -- 
thanks a lot!

Original comment by marcel.m...@tu-dortmund.de on 2 Nov 2011 at 9:25

• Changed state: Fixed