site-packages/docs/conf.py
site-packages/freyja-2025.post9.dist-info/INSTALLER
site-packages/freyja-2025.post9.dist-info/METADATA
site-packages/freyja-2025.post9.dist-info/RECORD
site-packages/freyja-2025.post9.dist-info/REQUESTED
site-packages/freyja-2025.post9.dist-info/WHEEL
site-packages/freyja-2025.post9.dist-info/direct_url.json
site-packages/freyja-2025.post9.dist-info/entry_points.txt
site-packages/freyja-2025.post9.dist-info/licenses/LICENSE
site-packages/freyja-2025.post9.dist-info/top_level.txt
site-packages/freyja/__init__.py
site-packages/freyja/_cli.py
site-packages/freyja/convert_paths2barcodes.py
site-packages/freyja/data/ARTIC_V4-1.bed
site-packages/freyja/data/NC_045512_Hu-1.fasta
site-packages/freyja/data/NC_045512_Hu-1.fasta.fai
site-packages/freyja/data/NC_045512_Hu-1.fasta.mmi
site-packages/freyja/data/NC_045512_Hu-1.gff
site-packages/freyja/data/agg_outputs.tsv
site-packages/freyja/data/aggregated_result.tsv
site-packages/freyja/data/colors.csv
site-packages/freyja/data/covariants_example.tsv
site-packages/freyja/data/covariants_plot.png
site-packages/freyja/data/curated_lineages.json
site-packages/freyja/data/dashboard_template.html
site-packages/freyja/data/example_query.csv
site-packages/freyja/data/introContent.txt
site-packages/freyja/data/last_barcode_update.txt
site-packages/freyja/data/lineage_mutations.json
site-packages/freyja/data/lineages.yml
site-packages/freyja/data/mixture.depth
site-packages/freyja/data/mixture.tsv
site-packages/freyja/data/mixture.vcf
site-packages/freyja/data/pathogen_config.yml
site-packages/freyja/data/plot_config.yml
site-packages/freyja/data/rel_growth_rates.csv
site-packages/freyja/data/sc2_regions_of_interest.json
site-packages/freyja/data/sc2_spike.csv
site-packages/freyja/data/sweep_metadata.csv
site-packages/freyja/data/sweep_metadata_missing.csv
site-packages/freyja/data/test.bam
site-packages/freyja/data/test.bam.bai
site-packages/freyja/data/test.depth
site-packages/freyja/data/test.pdf
site-packages/freyja/data/test.png
site-packages/freyja/data/test.tsv
site-packages/freyja/data/test.vcf
site-packages/freyja/data/test0.html
site-packages/freyja/data/test0.png
site-packages/freyja/data/test0_rel_growth_rates.csv
site-packages/freyja/data/test2.png
site-packages/freyja/data/testSummary.png
site-packages/freyja/data/test_filter.csv
site-packages/freyja/data/test_query.csv
site-packages/freyja/data/test_sweep.tsv
site-packages/freyja/data/times_metadata.csv
site-packages/freyja/data/times_metadata0.csv
site-packages/freyja/data/title.txt
site-packages/freyja/data/usher_barcodes.csv
site-packages/freyja/data/usher_barcodes.feather
site-packages/freyja/read_analysis_tools.py
site-packages/freyja/sample_deconv.py
site-packages/freyja/tests/__init__.py
site-packages/freyja/tests/test_barcoding.py
site-packages/freyja/tests/test_cli.py
site-packages/freyja/tests/test_deconv.py
site-packages/freyja/tests/test_read_analysis.py
site-packages/freyja/tests/test_utils.py
site-packages/freyja/tests/test_variants.py
site-packages/freyja/updates.py
site-packages/freyja/utils.py
