.codex
AGENTS.md
DEVELOPMENT.md
LICENSE
README.md
pyproject.toml
.github/workflows/publish-pypi.yml
__pycache__/__init__.cpython-312.pyc
__pycache__/__main__.cpython-312.pyc
__pycache__/cli.cpython-312.pyc
__pycache__/fetch.cpython-312.pyc
__pycache__/index.cpython-312.pyc
__pycache__/stats.cpython-312.pyc
lib/__pycache__/__init__.cpython-311.pyc
lib/__pycache__/__init__.cpython-312.pyc
lib/__pycache__/__init__.cpython-313.pyc
lib/__pycache__/__init__.cpython-39.pyc
lib/__pycache__/common.cpython-311.pyc
lib/__pycache__/common.cpython-312.pyc
lib/__pycache__/common.cpython-313.pyc
lib/__pycache__/common.cpython-39.pyc
lib/__pycache__/loginit.cpython-311.pyc
lib/__pycache__/loginit.cpython-312.pyc
lib/__pycache__/loginit.cpython-313.pyc
lib/__pycache__/loginit.cpython-39.pyc
mafutils/__init__.py
mafutils/__main__.py
mafutils/_version.py
mafutils/cli.py
mafutils/fetch.py
mafutils/index.py
mafutils/stats.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/top_level.txt
mafutils/__pycache__/__init__.cpython-312.pyc
mafutils/__pycache__/__main__.cpython-312.pyc
mafutils/__pycache__/cli.cpython-312.pyc
mafutils/__pycache__/fetch.cpython-312.pyc
mafutils/__pycache__/index.cpython-312.pyc
mafutils/__pycache__/stats.cpython-312.pyc
mafutils/lib/__init__.py
mafutils/lib/common.py
mafutils/lib/loginit.py
mafutils/lib/__pycache__/__init__.cpython-312.pyc
mafutils/lib/__pycache__/common.cpython-312.pyc
mafutils/lib/__pycache__/loginit.cpython-312.pyc
tests/crossblocks-missing-species.bed
tests/crossblocks.bed
tests/example.bed
tests/example.maf
tests/example.maf.block.idx
tests/example.maf.scaffold.idx
tests/example.maf.scaffold.regenerated.idx
tests/test_fetch.py
tests/__pycache__/test_fetch.cpython-312-pytest-8.4.1.pyc
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