Samtools style filtering syntax

[edawson]

Is there a way to use samtools style (i.e. decimal) filter expressions with sambamba? I expected that it would be supported (given that the human-readable version is surely built on top of it). I'm having to use massive command lines to do filtering and would rather use a four-digit decimal.

If you could point me towards the relevant manual page I've missed or let me know if it's possible that'd be great. The sort+filter operation is fantastic, and I'd love to keep using it, but without a flag->filter converter or a way to just use the flag I think I'll have to switch to samtools for this project.

[lomereiter]

Hi, this functionality was indeed missing. I've just added a new option --num-filter, which should be provided a string such as 96, /4 or 80/4 with meaning <-f samtools flag>/<-F samtools flag>.