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.gitignore
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bin/
*.paf
test/data/d1_*
test/data/d2_*
test/data/d3_*
test/data/d4_*
test/data/d5_*
test/data/*/*.fa
test/data/*/*.fasta
test/data/*/*.tar
test/data/*/*.tar.gz
test/data/*/fast5_files
test/data/*/slurm-*
/test/data/random_community/1_symbolic_links.sh
*/*.paf
test/evaluation/*/*/slurm*.out
test/evaluation/*/*/*.paf
test/evaluation/*/*/rawhash
test/evaluation/*/*/uncalled
test/evaluation/*/*/*.abundance
test/evaluation/*/*/*/slurm*.out
test/evaluation/*/*/*/*.paf
test/evaluation/*/*/*/rawhash
test/evaluation/*/*/*/uncalled
test/evaluation/*/*/*/*.abundance
test/evaluation/*/comparison/*.throughput
test/evaluation/*/comparison/*.paf
test/evaluation/*/comparison/*.comparison
test/evaluation/*/comparison/comparison.out
test/evaluation/*/comparison/comparison.err
test/evaluation/*/*/sigmap
test/evaluation/*/slurm*.out
test/evaluation/*/*.paf
test/evaluation/*/rawhash
test/evaluation/*/uncalled
test/evaluation/*/sigmap
test/evaluation/read_mapping/*/comparison/*.throughput
test/evaluation/read_mapping/*/comparison/*.paf
test/evaluation/read_mapping/*/comparison/*.comparison
test/evaluation/read_mapping/*/comparison/comparison.out
test/evaluation/read_mapping/*/comparison/comparison.err
test/*.paf
test/eval/*.paf
test/eval/*.time
test/eval/*.pt
test/eval/*.summary
./test/eval/slurm*.out
.vscode/
.DS_Store
*/.DS_Store
test/*.time
test/*.idx
src/*.o
gmon.out
rawhash-env
run_at.sh
rsync_to.sh
figures
alignment_scores.txt
extern/hdf5
extern/slow5lib
extern/kmer_models
baselines
**/outdir
**/throughput
results.txt
analyze_anchor_spacings.py
anchor_spacings.txt
paperfigures
*.ind
chains.txt
mapping_reasons.txt
read0_chains.txt