MANIFEST.in
setup.py
version.py
src/protect/__init__.py
src/protect/addons.py
src/protect/common.py
src/protect/mutation_translation.py
src/protect/rankboost.py
src/protect/version.py
src/protect.egg-info/PKG-INFO
src/protect.egg-info/SOURCES.txt
src/protect.egg-info/dependency_links.txt
src/protect.egg-info/entry_points.txt
src/protect.egg-info/not-zip-safe
src/protect.egg-info/requires.txt
src/protect.egg-info/top_level.txt
src/protect/alignment/__init__.py
src/protect/alignment/common.py
src/protect/alignment/dna.py
src/protect/alignment/rna.py
src/protect/binding_prediction/__init__.py
src/protect/binding_prediction/common.py
src/protect/binding_prediction/mhci.py
src/protect/binding_prediction/mhcii.py
src/protect/expression_profiling/__init__.py
src/protect/expression_profiling/rsem.py
src/protect/haplotyping/__init__.py
src/protect/haplotyping/phlat.py
src/protect/mutation_annotation/__init__.py
src/protect/mutation_annotation/snpeff.py
src/protect/mutation_calling/__init__.py
src/protect/mutation_calling/common.py
src/protect/mutation_calling/fusion.py
src/protect/mutation_calling/indel.py
src/protect/mutation_calling/muse.py
src/protect/mutation_calling/mutect.py
src/protect/mutation_calling/radia.py
src/protect/mutation_calling/somaticsniper.py
src/protect/mutation_calling/strelka.py
src/protect/pipeline/ProTECT.py
src/protect/pipeline/ProTECT_large.py
src/protect/pipeline/__init__.py
src/protect/pipeline/input_parameters.yaml
src/protect/qc/__init__.py
src/protect/qc/rna.py
src/protect/test/ci/__init__.py
src/protect/test/ci/test_protect.py
src/protect/test/unit/__init__.py
src/protect/test/unit/test_alignments.py
src/protect/test/unit/test_file_downloads.py
src/protect/test/unit/test_mhc_pathway_assessment.py
src/protect/test/unit/test_mutation_callers.py