.gitignore

# IDEs stuff
.idea/
.DS_Store
.vscode/
.ipynb_checkpoints

# Compiled / binaries
*.o
*.so
modules/chain_filter_by_id
modules/chain_score_filter
cesar
*.dSYM

# Python and temp stuff
__pycache__/*
modules/__pycache__/*
nextflow_logs/*

_*
TRASH/*
TESTS/*
temp/*
*.dat
*.ipynb
*.tar
*.log
*.bdb

# Para stuff
para/
lockFile.*

# mics
dasNov3/*
mm10/
mm10_merged/
RES/*
jobDir/*
chain_files/
chain_index/
250_mamm
rat_dat/
rat_omap_diff/
ML__old

# debug and test
micro_test_out/*
*.tsv
*.png
ML/.ipynb_checkpoints/
vs_Ensembl/.ipynb_checkpoints/
*.txt
*.hdf5
*.bst
test_output/*
for_paper/*
vs_Ensembl/
vs_Gloss_pipeline/
sandbox/
test-*/

2bits/
ANALYSIS/ENST00000320188.txt.ce
ANALYSIS/data/
ANALYSIS/dir_out/
ANALYSIS/gloss_data/
ANALYSIS/gloss_mut_comp/
ANALYSIS/inact_mut_check.py
ANALYSIS/loss_reports.tar
ANALYSIS/pseudo_cesar.tar
ANALYSIS/rev_out/
ANALYSIS/tab_file_to_cesar_in_OLD.py
ANALYSIS/tab_file_to_cesar_out.py
ANALYSIS_DUMP.tar
ML/
cesar_dir_rev/
gene_status/
myoLuc2_loss/
old_ANALYSIS/
test.fa
*/.ipynb_checkpoints/

*.2bit
afrotheria/
debug/
to_send/
modules/rn6_omap_debug/
modules/stdout
modules/old_orthology_type_map.py
models/data/
data_science/
.Rproj.user

defect_visualization/geneLossPipeOutput