support for adapters known to be ligated to the 3' end

[GoogleCodeExporter]

It should be possible to specify that an adapter should only be found in the 5' 
end or the 5' end of a sequence.

Original issue reported on code.google.com by marcel.m...@tu-dortmund.de on 1 Dec 2010 at 5:33

[GoogleCodeExporter]

That should of course read "in the 5' end or the 3' end of a sequence".

This issue was added in response to a user request which was based on a 
misunderstanding of the small RNA protocol that was used. The actual request 
should read:
It should be possible to specify that an adapter should only be found in the 3' 
end of a sequence. In other words, the knowledge that the adapter is always 
ligated to the 3' end should be used.

This has now been implemented: The -a parameter's default behavior is now to 
assume that the adapter was ligated to the 3' end. This is probably what most 
people want.

If you want the old behavior, use the -b option (see documentation for details).

Original comment by marcel.m...@tu-dortmund.de on 8 Dec 2010 at 11:36

• Changed title: support for adapters known to be ligated to the 3' end
• Changed state: Fixed