Tool to keep reads where all bases are above a specific quality score.

[max0479]

Hi. First I just discovered and tested your tool a few days ago. If my request has no sense or linked to something I didn't understand well, feel free to remove my message.

I would like to filter reads of FASTQ files to keep only very high quality sequences : reads where ALL bases are above Q30 by example. Two filter options seem to be appropriate :
-q QUALIFIED_QUALITY_PHRED --> set to "-q 30"
-u UNQUALIFIED_BASE_LIMIT --> would be logic to set "-u 0" to be sure to remove all reads where at least one base is under Q30. But sadly if you set "-u 0" in fact by default it do not filter reads by low quality base count at all (see -u UNQUALIFIED_BASE_LIMIT info). So I guess it is impossible to filter "perfect quality reads" (reads with no bases lower a specific quality). Default option to deactivate UNQUALIFIED_BASE_LIMIT should not be something other than 0?

Thanks a lot,
Max

[sfchen]

Thanks, good suggestion.

Currently it is

  -u UNQUALIFIED_BASE_LIMIT, --unqualified_base_limit=UNQUALIFIED_BASE_LIMIT
                        if exists more than unqualified_base_limit bases that
                        quality is lower than qualified quality, then this
                        read/pair is bad. Default 0 means do not filter reads
                        by low quality base count

So 0 will actually disable the unqualified_base filtering.

I will change default 0 to default -1.

[max0479]

Thank you very much for your feedback. That would be very useful for keeping only high quality reads.
Best regards,
Maxime