Closed xapple closed 11 years ago
We've fixed the issue, thanks for reporting it. We should have unittest for clean_reads, but we don't because it is a interface to the franklin library that we seldom use. We just created it because a colleague asked for an alternative interface to the library. Besides I don't think that we're going to implement those tests because we are now in the process of writing a new library from scratch with a new interface, that we think is more useful (you can also find this new code in github, it is called seq_crumbs). We would though accept contributions to improve any code, including unittests.
So I just tried
clean_reads
for processing my 454 reads, but am not sure I will continue using it as it is not working as advertised. It says in the documentation:So I ran this command:
But comparing the original file and the cleaned file outputed by
clean_reads
, I can see that all the reads are the same length. Now if the program ignored the-e
option who knows what other thing it is ignoring. I don't think I can trust such code. You should maybe consider adding some unittests for at least the basic functionality and options ?