AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
docs/Makefile
docs/authors.rst
docs/conf.py
docs/contributing.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/readme.rst
docs/usage.rst
tests/__init__.py
tests/test_io_ct.py
tests/test_tools_fastp.py
tests/test_tools_nextflow.py
tests/test_xlavir.py
tests/data/images/190px-Arthur-Pyle_Excalibur_the_Sword.JPG
tests/data/io/ct.ods
tests/data/io/ct.tsv
tests/data/io/ct.xlsx
tests/data/tools/consensus/Sample1.consensus.fa
tests/data/tools/consensus/Sample2.consensus.fa
tests/data/tools/consensus/Sample3.consensus.fa
tests/data/tools/fastp/Sample1.fastp.json
tests/data/tools/fastp/Sample2.fastp.json
tests/data/tools/mosdepth/Sample1.per-base.bed.gz
tests/data/tools/mosdepth/Sample2.per-base.bed.gz
tests/data/tools/mosdepth/Sample3.per-base.bed.gz
tests/data/tools/nextflow/execution_report.html
tests/data/tools/pangolin/pangolin.lineage_report.csv
tests/data/tools/samtools/Sample1.flagstat
tests/data/tools/samtools/Sample2.flagstat
tests/data/tools/samtools/Sample3.flagstat
tests/data/tools/variants/ivar/Sample3.snpsift.txt
tests/data/tools/variants/ivar/Sample3.vcf.gz
tests/data/tools/variants/nanopolish/Sample1.pass.vcf.gz
tests/data/tools/variants/nanopolish/Sample1.snpsift.txt
tests/data/tools/variants/nanopolish/Sample2.pass.vcf.gz
tests/data/tools/variants/nanopolish/Sample2.snpsift.txt
xlavir/__init__.py
xlavir/cli.py
xlavir/images.py
xlavir/util.py
xlavir/xlavir.py
xlavir.egg-info/PKG-INFO
xlavir.egg-info/SOURCES.txt
xlavir.egg-info/dependency_links.txt
xlavir.egg-info/entry_points.txt
xlavir.egg-info/not-zip-safe
xlavir.egg-info/requires.txt
xlavir.egg-info/top_level.txt
xlavir/io/__init__.py
xlavir/io/ct.py
xlavir/io/excel_sheet_dataframe.py
xlavir/io/xl.py
xlavir/qc/__init__.py
xlavir/qc/quality_requirements.py
xlavir/tools/__init__.py
xlavir/tools/consensus.py
xlavir/tools/fastp.py
xlavir/tools/mosdepth.py
xlavir/tools/nextclade.py
xlavir/tools/pangolin.py
xlavir/tools/samtools.py
xlavir/tools/variants.py
xlavir/tools/nextflow/__init__.py
xlavir/tools/nextflow/exec_report.py