privefl2

Question: position in extract full

2

I am trying to extract positions the same way as in pileup. I do this `pos = ifelse(mod_strand == ref_strand, ref_position, ifelse(ref_strand == "+", ref_position + 1, ref_position - 1))`...

Unexcepted output with modkit adjust-mods --convert h m

4

This is what I have for one read in the original BAM: ``` MM:Z:C+h?,3,0,0,2,1,0,9,4,4,0,2,2,1,2,3,5,0,0; C+m?,3,0,0,2,1,0,9,4,4,0,2,2,1,2,3,5,0,0; ML:B:C, 9,15,14,10,11,15, 6, 6, 7,11,16,10,10,11,11,18,16,18, 26,35,43,56,65,35,27,51,46,42,51,47,55,35,36,68,70,48 ``` This is what I get after ``` MM:Z:C+m?,3,0,0,2,1,0,9,4,4,0,2,2,1,2,3,5,0,0;...