ignoring substitution option

[yinshiyi]

I have a specific need to ignore substitution only events.
If a read have indel + substitution, I will count it as edited.
If a read have indel, I will count it as editted.
But if it only have substitution in the quantification window, I will not count it.
Do you have any suggestion on how to implement this function in amplican?
Thank you

[yinshiyi]

I am going to mess around with
events_filtered_shifted_normalized.csv

[yinshiyi]

awk -F',' 'NR==1 || $8=="mismatch"' ${output}/alignments/events_filtered_shifted_normalized.csv \
> ${output}/alignments/events_filtered_shifted_normalized_filtered.csv

after I filtered out all the events that are not mismatch

alignments<-read.csv(paste0(results_folder,"alignments/events_filtered_shifted_normalized_filtered.csv"))
# rerun the summarize function
amplicanSummarize(alignments[alignments$consensus & alignments$overlaps, ],read.csv(config))%>%select(ID,Reads_Edited)

I got all zeros in reads_edited
I think that the defaults pipeline does not consider mismatch as edits