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.gitignore
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# csv and files (there are a lot of them and they're ~28Mb each)
data/ord_covid
data/output
*.fasta
*.RData
*.RDS
*.rds
data/unc_covid/*.RDS
*.sam
data/sampled_covid
data/pangolineages
data/pangordlineages
data/unc_covid/metadata.tsv
data/zanini/*
*log.txt
src/df_tn93.RDS
data/output/sung_results_workspace.RData
.DS_Store
RTT/sequences.zip
*.zip
# Binaries and side-effects
RTT/FastTree
RTT/__pycache__/
nohup.out
# History files
.Rhistory
.Rapp.history
# Session Data files
.RData
!RTT/RTT_results.RData
src/*.RData
# Example code in package build process
*-Ex.R
# Output files from R CMD build
/*.tar.gz
# Output files from R CMD check
/*.Rcheck/
# RStudio files
.Rproj.user/
*.Rproj
# produced vignettes
vignettes/*.html
vignettes/*.pdf
# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth
# knitr and R markdown default cache directories
/*_cache/
/cache/
# Temporary files created by R markdown
*.utf8.md
*.knit.md
# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
rsconnect/
# LaTeX outputs:
*aux
*log
*gz
*bbl
*blg
*out&
ms/*.toc
drafts/Skeleton.aux
drafts/*out
*latexmk
*fls
ms/sup-supp.pdf
# Reads sequencing error simulations:
reads-seq-err/plot*.pdf
reads-seq-err/*.fastq
reads-seq-err/*_abundance.txt
# Sampling:
src/seqs/seqs*fasta*
src/trees/*.out
src/trees/*.nwk
src/trees/RAxML*.out*
src/raxml.out
# Plots:
src/Rplots.pdf
src/plot*.pdf
data/zanini/plot*.pdf
ms/figs/*pdf
# Trees generated:
src/trees/*.nwk
RTT/sampled_trees/
RTT/raw_tree/
# Drafts aux files
drafts/Skeleton.aux
drafts/Skeleton.blg
drafts/Skeleton.aux
drafts/Skeleton.log
drafts/Skeleton.out
drafts/Skeleton.tex
drafts/Skeleton_files/figure-latex/ordered_lik-1.pdf
drafts/Skeleton_files/figure-latex/sampled_bars-1.pdf
drafts/Skeleton_files/figure-latex/unnamed-chunk-1-1.pdf
ms/sup-ms.out
drafts/Skeleton.blg
drafts/Skeleton_files/figure-latex/prm.btshp-1.pdf
drafts/Skeleton_files/figure-latex/tree_distances-1.pdf
drafts/Skeleton.pdf
drafts/Skeleton_cache/*
# Root-To-Tip work
RTT/*.fasta
RTT/*.afa
RTT/*.fa
RTT/*.sam
RTT/*.fas*
# Sampled sequence intermediate results
RTT/*txt
!RTT/sampled_seqs.txt
RTT/*csv
!RTT/SRA_downloads.csv
!RTT/sampled_metadata.csv
RTT/samDONE/*
RTT/samBAD/*
/.directory
/src/parse-sam-c/sam2aln
/data/SraRunInfo_updated.csv
*.csv