LICENSE
MANIFEST.in
NOTICE
README.md
setup.py
mappgene/__init__.py
mappgene/cli.py
mappgene.egg-info/PKG-INFO
mappgene.egg-info/SOURCES.txt
mappgene.egg-info/dependency_links.txt
mappgene.egg-info/entry_points.txt
mappgene.egg-info/requires.txt
mappgene.egg-info/top_level.txt
mappgene/data/.DS_Store
mappgene/data/container/build.sh
mappgene/data/container/recipe.def
mappgene/data/example_inputs/example_MN908947_3_1_R1.fastq.gz
mappgene/data/example_inputs/example_MN908947_3_1_R2.fastq.gz
mappgene/data/extra_files/.DS_Store
mappgene/data/extra_files/ivar/.DS_Store
mappgene/data/extra_files/ivar/GCF_009858895.2_ASM985889v3_genomic.gff
mappgene/data/extra_files/ivar/nCoV-2019.bed
mappgene/data/extra_files/ivar/nCoV-2019.insert.bed
mappgene/data/extra_files/ivar/nCoV-2019.primer.bed
mappgene/data/extra_files/ivar/nCoV-2019.reference.fasta
mappgene/data/extra_files/ivar/nCoV-2019.scheme.bed
mappgene/data/extra_files/ivar/nCoV-2019.tsv
mappgene/data/extra_files/ivar/references/NC_045512.2.fasta
mappgene/data/extra_files/ivar/references/PS_1200bp.fasta
mappgene/data/extra_files/vpipe/.DS_Store
mappgene/data/extra_files/vpipe/vpipe.config
mappgene/data/extra_files/vpipe/vpipe.config.sars-cov-2-hpc
mappgene/data/extra_files/vpipe/references/.DS_Store
mappgene/data/extra_files/vpipe/references/NC_045512.2.fasta
mappgene/data/extra_files/vpipe/references/PS_1200bp.fasta
mappgene/data/extra_files/vpipe/references/cohort_consensus.fasta
mappgene/data/extra_files/vpipe/references/denovo_consensus.fasta
mappgene/subscripts/__init__.py
mappgene/subscripts/ivar.py
mappgene/subscripts/utilities.py
mappgene/subscripts/vpipe.py
tests/__init__.py
tests/ivar.py
tests/vpipe.py