/target
wfmash/
deps/
*.swp
*.swo
*~
.DS_Store

# Test outputs and temporary files
test_data/*.paf
test_data/*.png
test_data/*.fai
*.paf
*.1aln
*.png
*.log
*.html

# FASTA files (except the compressed reference)
*.fa
*.fasta
*.fai
*.fa.gz
!data/scerevisiae8.fa.gz
!data/B-3106.fa
*.fa.gz.fai
*.fa.gz.gzi

# Index and intermediate files
*.gdb
*.gix
*.ktab*
*.bps
*.[0-9]gdb

# Temporary test files
/tmp/
x.paf
y.fa
z.paf
v.fa
test_*.fa
test_*.paf
dummy.fa
minimal.fa
all_seqs.fa
s288c*.fa

# Wfmash temp files
wfmash-*

# Except the input test files we want to keep
!test_data/chrV.fastga.paf
!test_data/chrV.wfmash.paf

# Golden test output files (generated by tests/golden_data/generate_golden.sh)
tests/golden_data/*.1aln
tests/golden_data/*.paf
