abcoxyzide
commented
9 months ago - modified mbias plots to always start at 5' end of the read (ie 5' of original strand for R1, and 3' of original strand for R2), instead of going from upstream to downstream according to reference genome
- accordingly, added option to trim reads based on distance from 5' and 3' ends
- modified extract subcommand to give 4-nucleotide context for CpG sites
- added a filter option based on insert size
- modified the output format of perRead subcommand