Read minimum lengths: Include read names in rest file?

[marcelm]

From cas...@gmail.com on March 07, 2012 11:29:15

If I use trim and apply a minimum length, then the rest file contains the trimmed part for sequences not in the output file. So I cannot tell which line in the rest file corresponds to a line in the output.

I would suggest adding the sequence name to the rest file: jamescasbon@8ace754

Original issue: http://code.google.com/p/cutadapt/issues/detail?id=37

[marcelm]

From marcel.m...@tu-dortmund.de on March 09, 2012 03:04:01

I think this is really useful, but I’m reluctant to change the file format (as bad as it is) because it wouldn’t be backwards compatible. Perhaps some scripts are already out there that rely on this. My idea for a while has been to add a new --info-file option that would also contain the "rests", but also the read name, no. of mismatches, length of the overlap etc.

But perhaps no one is really using the rest file in an automated way, I don’t know.

[marcelm]

From marcel.m...@tu-dortmund.de on June 17, 2012 10:28:53

I've merged your changes, let's see who complains. By the way, to make collaboration easier, I've now moved the source code to github: https://github.com/marcelm/cutadapt . Thanks for the patch!

Status: Fixed