simplified reporting option · Issue #112 · marcelm/cutadapt (original) (raw)

Hello,

Lately I have been using cutadapt as part of batch scripts processing dozens of FASTQ files at a time. I wanted a simpler output from cutadapt for the sake of more easily checking the pre-processing steps. Originally I was going to parse the default verbose report format from cutadapt, but decided it would be just as quick and more useful to patch cutadapt directly to add such an option. I have posted a patch here:

https://gist.github.com/jvolkening/c34e1258dc8ac905dba5

It adds a "--succinct" option which tells cutadapt to output a single, tab-delimited report with a minimum of relevant fields so that, for instance, multiple sequential calls to cutadapt will produce a tab-delimited table of report data rather than a long text file. Feel free to either ignore or incorporate as you see fit. I should note that Python is not my first language, and that the patch has not been extensively tested. I will report back if I find any problems with further regular usage.

Regards,
Jeremy