bin/samtools-1.22.1/
venv/*
*.log
nohup.out

# Files generated during data processing
*.txt
*.pod5
*.bam
*.bam.bai
*.blow5
*.blow5.idx
*.fastq
*.fastq.index
*.fastq.index.fai
*.fastq.index.gzi

*.svg
*.xlsx

01_data/dna_giab/*.fa
01_data/subsets/*

02_compare_time/logs/*.log
02_compare_time/results/*.json
02_compare_time/scripts/jobs/*.sh
02_compare_time/stdout/*.stdOut
02_compare_time/stdout/*.stdErr
02_compare_time/tmp/*
!02_compare_time/tmp/.gitkeep

03_compare_alignments/alignments/*.tsv
03_compare_alignments/alignments/*.parquet
03_compare_alignments/alignments_parsed/*.tsv
03_compare_alignments/alignments_merged/*.parquet
03_compare_alignments/alignments_compared/*.parquet

04_m1a_analysis/alignments/*.parquet
04_m1a_analysis/reformatted/*.parquet
04_m1a_analysis/pickle_files/*.pkl