.gitignore

src_tools_evaluation/
splam.zip
splam/
train/src/archive/
experiments/archive/
train/junctions/
train/

# sys
__pycache__/
.DS_Store
.vscode

# main dirs
Dataset/
sc/longformer/
slides/
results/
paper
src_spliceNN/
SPLAM_C++/
test/
spliceai_result*
*_output/
src/tmp_out/
splam.egg-info/
dist/
build/
private/

# train 
train/src/MODEL*
train/src/MODEL/
train/src/MODEL_TEST/
train/src/INPUTS/Intersection/
train/src/Conformer/
train/src/Conformer/.git/
train/src/block-recurrent-transformer/
train/src/BAM_REF_Intersection/
train/src/INPUTS/
train/src/Experiment_SpliceAI/INPUTS/
train/src/Experiment_SpliceAI/models/
train/src/prev/
train/src/prev_MODEL/
train/src/5_GET_BAM_NEG_JUNCS/BAM_junctions/
train/src/6_GET_BAM_NEG_OPP_STRAND_JUNCS/BAM_junctions/


# benchmark 
benchmark/src_tools_evaluation/spliceai_result*
benchmark/src_tools_evaluation/splam_result/
benchmark/src_tools_evaluation/prev_res/
benchmark/src_tools_evaluation/Ida/
benchmark/src_tools_evaluation/dataset/
benchmark/src_tools_evaluation/IMG/
benchmark/src_tools_evaluation/1st_res_noparalog/
benchmark/src_tools_evaluation/splam_result_prev/
benchmark/src_splam_cleanup/results/*
benchmark/src_splam_cleanup_STAR/results/*
benchmark/src_generalization_test/figures/**/*.png
benchmark/src_generalization_test/figures/heatmap/25000-25000/

# filetypes
*.pptx
*.gff
*.gff3
*.db
*.tsv
*.pkl
*.bed
*.fa
*.fai
*.csv
*.pdf
TODO