28 Jul
2011
28 Jul
'11
4:26 p.m.
Hello Peter and all, Peter Cock wrote, On 07/28/2011 05:08 PM:
It concerns me that you're doing this for both "fastqillumina" format (good) and "fastqsolexa" (bad). Treating the later as fastqillumina would give negative scores and probably cause trouble. Unless BWA copes but if so it is a poor choice of argument name?
In the XML wrapper you've not updated the help text for the FASTQ parameters to indicate it would now accept Illumina FASTQ as well as Sanger FASTQ.
Peter
P.S. It is a patch file, but it has extension xml??
These are all valid comments, here's an updated patch (with a ".patch" extension :) ). Thanks! -gordon