.gitignore
CHANGELOG.md
CITATION.cff
LICENSE
README.md
docs-requirements.txt
env.yml
mkdocs.yml
pyproject.toml
sonar-project.properties
test-requirements.txt
test-requirements.yaml
.github/workflows/publish.yaml
.github/workflows/release.yml
.github/workflows/sync.yml
.github/workflows/tests.yaml
AmpliGone/__init__.py
AmpliGone/__main__.py
AmpliGone/alignmentmatrix.py
AmpliGone/alignmentpreset.py
AmpliGone/args.py
AmpliGone/cut_reads.py
AmpliGone/cutlery.py
AmpliGone/fasta2bed.py
AmpliGone/io_ops.py
AmpliGone/log.py
AmpliGone.egg-info/PKG-INFO
AmpliGone.egg-info/SOURCES.txt
AmpliGone.egg-info/dependency_links.txt
AmpliGone.egg-info/entry_points.txt
AmpliGone.egg-info/requires.txt
AmpliGone.egg-info/top_level.txt
docs/amplicon-types.md
docs/index.md
docs/installation.md
docs/user-guide.md
docs/img/amplicon-type_end-to-end.png
docs/img/amplicon-type_end-to-mid.png
docs/img/amplicon-type_fragmented.png
docs/img/virtual_primer.png
tests/__init__.py
tests/config.yaml
tests/data/expected_outputs/sars-cov-2-eo.fastq
tests/data/expected_outputs/synthetic-eo.fastq
tests/data/expected_outputs/too-short-eo.fastq
tests/data/inputs_outputs/corrupted.fastq
tests/data/inputs_outputs/empty.fastq
tests/data/inputs_outputs/influenza.fastq
tests/data/inputs_outputs/sars-cov-2.fastq
tests/data/inputs_outputs/synthetic.fastq
tests/data/inputs_outputs/too-short.fastq
tests/data/inputs_outputs/wrong_format.fastq
tests/data/primers/ARTIC-V5.3.2.fasta
tests/data/primers/SARS-CoV-2-ARTIC-V5.3.2.scheme.bed
tests/data/primers/empty.fasta
tests/data/primers/synthetic-no-match.fasta
tests/data/primers/synthetic.bed
tests/data/primers/synthetic.fasta
tests/data/references/SARS-CoV-2-reference.fasta
tests/data/references/empty.fasta
tests/data/references/indexed_ref.mmi
tests/data/references/synthetic.fasta
tests/e2e/__init__.py
tests/e2e/config_parser.py
tests/e2e/test_e2e.py
tests/unit/test_args.py
tests/unit/test_cut_reads.py
tests/unit/test_cutlery.py
tests/unit/test_fasta2bed.py