lehner-lab/DiMSum: Haam Seui Gok

Major updates: New command-line argument "--synonymSequencePath" in order to supply additional reference variants (other than the wild-type) for which synonymous substitution variant fitness and error estimates are required "all_variants" R object now excludes synonymous variants for coding sequences (i.e. only WT and missense mutations); these are instead included in the "synonymous" R object (previously "silent" R object) "fitness_doubles.txt" output file now contains all doubles (not just those where both constituent singles were quantified) Minor updates: Synonymous variant fitness and error estimates are now provided when "--mixedSubstitutions" option set to TRUE Synonymous variants saved to "fitness_synonymous.txt"( instead of "fitness_silent.txt"), WT nucleotide variant is included as well as all sample read counts "fitness_wildtype.txt" now contains all sample read counts Fixed bug in "dimsum__concatenate_reads" Updated checks on count and barcode identity file