edge_trim not working

[xapple]

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:

 -e, -edge_trim edge trimming values
 The number of nucleotides to be removed from the sequence beginning and end. This would be an unconditional trimming. The number of nucleotides should be given as two integers separated by a comma (e.g. 0,10).

So I ran this command:

 clean_reads -i ./reads1.fastq -o ./reads1.clean.fastq -p 454 -f fastq -e 10,0

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 ?

[JoseBlanca]

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.