LICENSE
README.md
setup.py
freyja/__init__.py
freyja/_cli.py
freyja/convert_paths2barcodes.py
freyja/read_analysis_tools.py
freyja/sample_deconv.py
freyja/updates.py
freyja/utils.py
freyja.egg-info/PKG-INFO
freyja.egg-info/SOURCES.txt
freyja.egg-info/dependency_links.txt
freyja.egg-info/entry_points.txt
freyja.egg-info/requires.txt
freyja.egg-info/top_level.txt
freyja/data/NC_045512_Hu-1.fasta
freyja/data/NC_045512_Hu-1.fasta.fai
freyja/data/NC_045512_Hu-1.fasta.mmi
freyja/data/NC_045512_Hu-1.gff
freyja/data/agg_outputs.tsv
freyja/data/aggregated_result.tsv
freyja/data/colors.csv
freyja/data/curated_lineages.json
freyja/data/dashboard_template.html
freyja/data/example_covariants.tsv
freyja/data/example_covariants_plot.png
freyja/data/example_query.csv
freyja/data/introContent.txt
freyja/data/last_barcode_update.txt
freyja/data/lineages.yml
freyja/data/mixture.depth
freyja/data/mixture.tsv
freyja/data/plot_config.yml
freyja/data/rel_growth_rates.csv
freyja/data/sweep_metadata.csv
freyja/data/sweep_metadata_missing.csv
freyja/data/test.bam
freyja/data/test.bam.bai
freyja/data/test.pdf
freyja/data/test.png
freyja/data/test.vcf
freyja/data/test0.html
freyja/data/test0.png
freyja/data/test0_rel_growth_rates.csv
freyja/data/test2.png
freyja/data/testSummary.png
freyja/data/test_filter.csv
freyja/data/test_query.csv
freyja/data/test_sweep.tsv
freyja/data/times_metadata.csv
freyja/data/times_metadata0.csv
freyja/data/title.txt
freyja/data/usher_barcodes.csv
freyja/data/usher_barcodes_with_gisaid.csv
freyja/tests/__init__.py
freyja/tests/test_barcoding.py
freyja/tests/test_deconv.py
freyja/tests/test_read_analysis.py
freyja/tests/test_utils.py
freyja/tests/test_variants.py