LICENSE
MANIFEST.in
README.md
pyproject.toml
src/hlaont/__init__.py
src/hlaont/cli.py
src/hlaont.egg-info/PKG-INFO
src/hlaont.egg-info/SOURCES.txt
src/hlaont.egg-info/dependency_links.txt
src/hlaont.egg-info/entry_points.txt
src/hlaont.egg-info/requires.txt
src/hlaont.egg-info/top_level.txt
src/hlaont/input/__init__.py
src/hlaont/input/bam.py
src/hlaont/input/fastq.py
src/hlaont/input/phasing.py
src/hlaont/input/regions.py
src/hlaont/resources/__init__.py
src/hlaont/resources/genes.yaml
src/hlaont/resources/anchors/__init__.py
src/hlaont/resources/anchors/anchors.fa.gz
src/hlaont/resources/anchors/anchors.meta.tsv.gz
src/hlaont/resources/anchors/anchors_manifest.json
src/hlaont/resources/anchors/build.py
src/hlaont/resources/anchors/prepare_candidates.py
src/hlaont/resources/anchors/vendor/136ref.fa.gz
src/hlaont/resources/anchors/vendor/FUFIHLA_LICENSE
src/hlaont/resources/anchors/vendor/NOTICE.md
src/hlaont/resources/controls/__init__.py
src/hlaont/resources/controls/build.py
src/hlaont/resources/controls/c4_flanked_forms.chm13v2.fa.gz
src/hlaont/resources/controls/chr17_control.chm13v2.fa.gz
src/hlaont/resources/models/__init__.py
src/hlaont/resources/models/build_c4_form_signature.py
src/hlaont/resources/models/c4_form_signature.yaml
src/hlaont/resources/models/c4_joint_call.yaml
src/hlaont/resources/models/read_error_ont_r10.yaml
src/hlaont/resources/models/stage0_fastq_sieve.yaml
src/hlaont/resources/models/stage4_typing.yaml
src/hlaont/resources/models/vendor/BADREAD_LICENSE
src/hlaont/resources/models/vendor/NOTICE.md
src/hlaont/resources/models/vendor/nanopore2023.gz
src/hlaont/resources/regions/alt_contigs.chm13v2.yaml
src/hlaont/resources/regions/alt_contigs.grch38.yaml
src/hlaont/resources/regions/mhc_window.chm13v2.bed
src/hlaont/resources/regions/mhc_window.grch38.bed
src/hlaont/resources/templates/__init__.py
src/hlaont/resources/templates/assembly_sources.py
src/hlaont/resources/templates/build.py
src/hlaont/resources/templates/build_assembly_bundle.py
src/hlaont/resources/templates/build_c4_bundle.py
src/hlaont/resources/templates/sources.py
src/hlaont/resources/templates/assembly_bundle/bundle.fa.gz
src/hlaont/resources/templates/assembly_bundle/bundle.meta.tsv.gz
src/hlaont/resources/templates/assembly_bundle/bundle.models.jsonl.gz
src/hlaont/resources/templates/assembly_bundle/bundle_manifest.json
src/hlaont/resources/templates/assembly_bundle/c4.fa.gz
src/hlaont/resources/templates/assembly_bundle/c4.meta.tsv.gz
src/hlaont/resources/templates/assembly_bundle/c4.models.jsonl.gz
src/hlaont/resources/templates/assembly_bundle/c4_bundle_manifest.json
src/hlaont/stages/__init__.py
src/hlaont/stages/align_depth.py
src/hlaont/stages/assign.py
src/hlaont/stages/c4_chr17_cn.py
src/hlaont/stages/c4_cn.py
src/hlaont/stages/c4_form.py
src/hlaont/stages/chr17_control.py
src/hlaont/stages/cn.py
src/hlaont/stages/consensus.py
src/hlaont/stages/error_model.py
src/hlaont/stages/genotype.py
src/hlaont/stages/hla_typing.py
src/hlaont/stages/novelty.py
src/hlaont/stages/output.py
src/hlaont/stages/pipeline.py