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.gitignore
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.gitignore
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# Exclude OSX-specific files
.DS_Store
# Exclude intermediate/temp Emacs/editor files
*~
*#
.#*
# Exclude locally-built documentation
docs/_build
docs/_static
docs/_templates
# Exclude distribution-related files
build/
*.egg-info/
dist/
# Exclude test input
tests/test_input/sequences/GC*_concat*
# Exclude test output
tests/test_output
# Files created during testing, but not in tests/test_output
tests/test_input/sequences/test_stitch_concat.fas
tests/test_input/sequences/test_stitch_noambig.fas
tests/test_input/eprimer3/GCF_000696465.1_named_screened.fasta
tests/test_input/eprimer3/GCF_000696465.1_named_screened.json
tests/test_input/eprimer3/GCF_000740965.1_concat_named_screened.fasta
tests/test_input/eprimer3/GCF_000740965.1_concat_named_screened.json
tests/test_input/eprimer3/GCF_000749965.1_concat_named_screened.fasta
tests/test_input/eprimer3/GCF_000749965.1_concat_named_screened.json
tests/test_input/sequences/GCF_000011605.1_prodigal.fasta
tests/test_input/sequences/GCF_000024645.1_prodigal.fasta
tests/test_input/sequences/GCF_000260925.1_prodigal.fasta
tests/test_input/sequences/GCF_000696465.1_prodigal.fasta
tests/test_input/sequences/*.bedgenome
tests/test_input/sequences/*.fai
# Exclude walkthrough output
tests/walkthrough/*.json
tests/walkthrough/blastn
tests/walkthrough/deduped
tests/walkthrough/eprimer3
tests/walkthrough/prodigal
tests/walkthrough/sequences/*concat*
tests/walkthrough/test.log
tests/walkthrough/primersearch/
tests/walkthrough/classify
tests/walkthrough/extract
tests/walkthrough/plot
tests/walkthrough/config
tests/walkthrough/blastn_cds/
tests/walkthrough/blastn_igr/
tests/walkthrough/classify_cds/
tests/walkthrough/classify_igr/
tests/walkthrough/deduped_cds/
tests/walkthrough/deduped_igr/
tests/walkthrough/extract_cds/
tests/walkthrough/extract_igr/
tests/walkthrough/primersearch_cds/
tests/walkthrough/primersearch_igr/
tests/walkthrough/prodigaligr/
tests/walkthrough/sequences/GCF_000011605.1.bedgenome
# Exclude Python files
*.pyc
__pycache__/
# Exclude developers' virtualenvs
venv-*
# Exclude local coverage output
.coverage*
cover/
# Exclude Jupyter works in progress
.ipynb_checkpoints
*.ipynb
# Exclude VS Code config
.vscode