.git-blame-ignore-revs
.gitignore
.readthedocs.yaml
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
PlasMAAG/__init__.py
PlasMAAG/__main__.py
PlasMAAG/click_file_types.py
PlasMAAG/command_line_runners.py
PlasMAAG/environment.py
PlasMAAG/richclick_options.py
PlasMAAG/snakefile.smk
PlasMAAG/envs/PlasMAAG.yaml
PlasMAAG/envs/genomad.yaml
PlasMAAG/envs/node2vec.yaml
PlasMAAG/envs/spades_env.yaml
PlasMAAG/envs/strobe_env.yaml
PlasMAAG/files_used_in_snakemake_workflow/__init__.py
PlasMAAG/files_used_in_snakemake_workflow/circularisation.py
PlasMAAG/files_used_in_snakemake_workflow/classify_bins_with_geNomad.py
PlasMAAG/files_used_in_snakemake_workflow/concatenate.py
PlasMAAG/files_used_in_snakemake_workflow/embeddings_to_neighs.py
PlasMAAG/files_used_in_snakemake_workflow/fastnode2vec_args.py
PlasMAAG/files_used_in_snakemake_workflow/git_commit.py
PlasMAAG/files_used_in_snakemake_workflow/merge_assembly_alignment_graphs.py
PlasMAAG/files_used_in_snakemake_workflow/merge_circular_plamb_clusters.py
PlasMAAG/files_used_in_snakemake_workflow/process_blastout.py
PlasMAAG/files_used_in_snakemake_workflow/process_gfa.py
PlasMAAG/files_used_in_snakemake_workflow/write_candidate_bins.py
PlasMAAG_core.egg-info/PKG-INFO
PlasMAAG_core.egg-info/SOURCES.txt
PlasMAAG_core.egg-info/dependency_links.txt
PlasMAAG_core.egg-info/entry_points.txt
PlasMAAG_core.egg-info/requires.txt
PlasMAAG_core.egg-info/top_level.txt
config/config.yaml
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/encode_n2v_asimetric.py
vamb/git_commit.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