.codex
.gitignore
AGENTS.md
DEVELOPMENT.md
LICENSE
README.md
THIRD_PARTY_LICENSES.md
pyproject.toml
.github/workflows/publish-pypi.yml
benchmarks/README.md
benchmarks/Snakefile
benchmarks/baseline-manual-timings.txt
benchmarks/config.yaml
benchmarks/history.csv
benchmarks/notebook.ipynb
benchmarks/parse_benchmarks.py
benchmarks/rulegraph.png
benchmarks/profiles/slurm/config.yaml
mafutils/__init__.py
mafutils/__main__.py
mafutils/_version.py
mafutils/cli.py
mafutils/fetch.py
mafutils/gc.py
mafutils/index.py
mafutils/stats.py
mafutils/validate.py
mafutils.egg-info/PKG-INFO
mafutils.egg-info/SOURCES.txt
mafutils.egg-info/dependency_links.txt
mafutils.egg-info/entry_points.txt
mafutils.egg-info/requires.txt
mafutils.egg-info/scm_file_list.json
mafutils.egg-info/scm_version.json
mafutils.egg-info/top_level.txt
mafutils/lib/__init__.py
mafutils/lib/bgzf.py
mafutils/lib/common.py
mafutils/lib/loginit.py
tests/crossblocks-missing-species.bed
tests/crossblocks.bed
tests/example-tabs.maf
tests/example-tabs.maf.block.idx
tests/example-tabs.maf.scaffold.idx
tests/example.bed
tests/example.maf
tests/example.maf.bgz
tests/example.maf.bgz.block.idx
tests/example.maf.bgz.scaffold.idx
tests/example.maf.block.idx
tests/example.maf.gz
tests/example.maf.gz.block.idx
tests/example.maf.gz.scaffold.idx
tests/example.maf.scaffold.idx
tests/example.maf.scaffold.regenerated.idx
tests/test_compression.py
tests/test_fetch.py
tests/test_gc.py
tests/test_validate.py
tests/expected-fasta/01-singleblock-gap.fa
tests/expected-fasta/02-truncatedblock.fa
tests/expected-fasta/03-crossblocks-missing.fa
tests/expected-fasta/04-singleblock.fa
tests/expected-fasta/05-crossblocks.fa
tests/expected-fasta/06-noalign.fa
tests/expected-fasta/07-negstrand.fa
tests/expected-fasta/08-span-multiple-gaps.fa
tests/expected-fasta/09-missingchrom.fa
tests/expected-fasta/10-crossblocks-missing-species.fa
tests/expected-maf/01-singleblock-gap.maf
tests/expected-maf/02-truncatedblock.maf
tests/expected-maf/03-crossblocks-missing.maf
tests/expected-maf/04-singleblock.maf
tests/expected-maf/05-crossblocks.maf
tests/expected-maf/06-noalign.maf
tests/expected-maf/07-negstrand.maf
tests/expected-maf/08-span-multiple-gaps.maf
tests/expected-maf/09-missingchrom.maf
tests/expected-maf/10-crossblocks-missing-species.maf