additionalMods reduction, improved predicted mods discovery and isodecoder name shortening

Updates

• 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