.gitignore

.*
!.git*
_*
*.out
~$*

!.nojekyll

results*/*

!results*/synonymous_mut_rates
results*/synonymous_mut_rates/*
!results*/synonymous_mut_rates/rates_by_clade.csv

!results*/mutation_counts
results*/mutation_counts/*
!results*/mutation_counts/aggregated.csv

!results*/clade_founder_nts
results*/clade_founder_nts/*
!results*/clade_founder_nts/clade_founder_nts.csv
!results*/clade_founder_nts/clade_founder_aas.csv

!results*/expected_vs_actual_mut_counts
results*/expected_vs_actual_mut_counts/*
!results*/expected_vs_actual_mut_counts/expected_vs_actual_mut_counts.csv

!results*/aa_fitness
results*/aa_fitness/*
!results*/aa_fitness/aamut_fitness_all.csv
!results*/aa_fitness/aamut_fitness_by_clade.csv
!results*/aa_fitness/aamut_fitness_by_subset.csv
!results*/aa_fitness/aa_fitness.csv
!results*/aa_fitness/aa_fitness.json.gz

!results*/nt_fitness
results*/nt_fitness/*
!results*/nt_fitness/ntmut_fitness_all.csv
!results*/nt_fitness/ntmut_fitness_by_clade.csv
!results*/nt_fitness/ntmut_fitness_by_subset.csv
!results*/nt_fitness/nt_fitness.csv
!results*/nt_fitness/synonymous_constraint_figure.pdf

!results*/dms
results*/dms/*/*
!results*/dms/*/processed.csv

!results*/dms-viz
results*/dms-viz/*
!results*/dms-viz/mut_fitness.json

tmp/