varforge 0.1.0

Synthetic cancer sequencing test data generator
Documentation 
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/target
.claude/

# Large genomic output files
*.bam
*.bai
*.fastq.gz
*.fq.gz
*.vcf.gz
*.tbi
*.fa
*.fasta
*.fai
*.csi
# Reference index files (bwa-mem2, GATK, RTG)
*.dict
*.0123
*.amb
*.ann
*.bwt.2bit.64
*.pac
*.sdf/
**/*.sdf/

# Old benchmark output (superseded by benchmarking/)
benchmark_output/

# LaTeX build artifacts — intermediate PDFs (named PDFs go in docs/paper/pdfs/)
docs/paper/main.pdf
docs/paper/main_big.pdf
docs/paper/main_2col.pdf
docs/paper/main_2p.pdf

# LaTeX auxiliary files
docs/paper/*.aux
docs/paper/*.bbl
docs/paper/*.blg
docs/paper/*.log
docs/paper/*.out
docs/paper/*.toc
docs/paper/*.bcf
docs/paper/*.run.xml
docs/paper/main.bbl-SAVE-ERROR

# Benchmark timing files (raw data, not needed in repo)
benchmarking/results/tables/*.txt

# Downstream VC benchmark results (large, generated locally)
benchmarking/downstreamvc/results/*/