LICENSE.txt
MANIFEST.in
README.md
VERSION
requirements.txt
setup.cfg
setup.py
PHEnix.egg-info/PKG-INFO
PHEnix.egg-info/SOURCES.txt
PHEnix.egg-info/dependency_links.txt
PHEnix.egg-info/requires.txt
PHEnix.egg-info/top_level.txt
phe/__init__.py
phe/annotations/CoverageAnnotator.py
phe/annotations/__init__.py
phe/mapping/BWAMapper.py
phe/mapping/Bowtie2Mapper.py
phe/mapping/__init__.py
phe/mapping/mapping_factory.py
phe/metadata/__init__.py
phe/utils/__init__.py
phe/utils/reader.py
phe/variant/GATKVariantCaller.py
phe/variant/MPileupVariantCaller.py
phe/variant/__init__.py
phe/variant/variant_factory.py
phe/variant_filters/ADFilter.py
phe/variant_filters/DP4Filter.py
phe/variant_filters/DepthFilter.py
phe/variant_filters/GQFilter.py
phe/variant_filters/GTFilter.py
phe/variant_filters/MQ0FFilter.py
phe/variant_filters/MQ0Filter.py
phe/variant_filters/MQFilter.py
phe/variant_filters/QualFilter.py
phe/variant_filters/__init__.py
scripts/filter_vcf.py
scripts/phenix.py
scripts/prepare_reference.py
scripts/run_snp_pipeline.py
scripts/vcf2distancematrix.py
scripts/vcf2fasta.py
scripts/vcf2json.py