.git-blame-ignore-revs
.gitignore
.readthedocs.yaml
CHANGELOG.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
.github/ISSUE_TEMPLATE.md
.github/workflows/cli_vamb.yml
.github/workflows/lint.yml
.github/workflows/snakemake_avamb.yml
.github/workflows/unittest.yml
doc/README.md
doc/conf.py
doc/front_page.md
doc/histogram.npz
doc/how_to_run.md
doc/index.rst
doc/inputs_outputs.md
doc/installation.md
doc/tips.md
src/_vambtools.pyx
src/concatenate.py
src/create_fasta.py
src/create_kernel.py
test/test_aamb_encode.py
test/test_cluster.py
test/test_encode.py
test/test_parsebam.py
test/test_parsecontigs.py
test/test_parsemarkers.py
test/test_reclustering.py
test/test_results.py
test/test_semisupervised_encode.py
test/test_vambtools.py
test/testtools.py
test/data/fasta.fna
test/data/marker.fna
test/data/aemb/6.aemb.tsv
test/data/aemb/7.aemb.tsv
test/data/aemb/8.aemb.tsv
test/data/bam/10.bam
test/data/bam/11.bam
test/data/bam/12.bam
vamb/__init__.py
vamb/__main__.py
vamb/aamb_encode.py
vamb/cluster.py
vamb/encode.py
vamb/hloss_misc.py
vamb/kernel.npz
vamb/marker.hmm
vamb/parsebam.py
vamb/parsecontigs.py
vamb/parsemarkers.py
vamb/reclustering.py
vamb/semisupervised_encode.py
vamb/taxonomy.py
vamb/taxvamb_encode.py
vamb/vambtools.py
vamb.egg-info/PKG-INFO
vamb.egg-info/SOURCES.txt
vamb.egg-info/dependency_links.txt
vamb.egg-info/entry_points.txt
vamb.egg-info/requires.txt
vamb.egg-info/top_level.txt
workflow_avamb/README.md
workflow_avamb/avamb.snake.conda.smk
workflow_avamb/config.json
workflow_avamb/envs/avamb.yaml
workflow_avamb/envs/checkm2.yml
workflow_avamb/envs/minimap2.yaml
workflow_avamb/envs/samtools.yaml
workflow_avamb/src/abundances_mask.py
workflow_avamb/src/create_abundances.py
workflow_avamb/src/create_cluster_scores_bin_path_dict.py
workflow_avamb/src/manual_drep_JN.py
workflow_avamb/src/mv_bins_from_mdrep_clusters.py
workflow_avamb/src/rip_bins.py
workflow_avamb/src/transfer_contigs_and_aggregate_all_nc_bins.py
workflow_avamb/src/update_cluster_scores_dict_after_ripping.py
workflow_avamb/src/workflow_tools.py
workflow_avamb/src/write_abundances.py
workflow_avamb/src/write_clusters_from_dereplicated_and_ripped_bins.sh