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Reduced additional mods file to contain only inosine 34. This allows mim-tRNAseq to discover and annotate other mods on its own and reduces misalignment, e.g. human Asp-GTC-3
New mods discovered after round 1 of alignment are then subtracted from predictedMods so that their validity can be rechecked after alignment improvements in round 2. Only these are then added to predictedMods
Isodecoder names now exclude 2nd number in name (except "chr" containing names) in all outputs and plots
Stops and misinc heatmaps no longer plot gap information ("-")
knownMods.csv renamed to allMods.csv as it includes Modomics, additionalMods, and predictedMods sites
Bugfixes
allMods.csv positions now 1-based
--misinc-thresh now used for heatmap row annotations (i.e. stop and misinc site counts)
Duplicates in countTable no longer removes as pandas issue removes non-duplicated rows