Panagiotis Papasaikas

For completeness when using call-mods + pileup using the same filtering thresholds I get identical results as when using pileup with --no-filtering so: ``` modkit call-mods -p 0.2 --mod-threshold a:0.8...

Thank you for the quick reply. You are right, that was a copy pasting error on my side. For pileup_B (pileup only bed generation) it should be: `modkit pileup -p...

I followed the suggested procedure: `# [src/command_utils.rs::117][2024-02-16 21:05:56][DEBUG] estimated pass threshold 0.7324219 for primary sequence base A` Then created the two pileups: ``` modkit call-mods --filter-threshold 0.7324219 --mod-threshold a:0.8 input.bam...

Just following up on the same issue. Using v0.3.0 and modkit extract with --include-bed is very sluggish (1h for a couple tenths of bed lines). It's actually way faster to...