├── .editorconfig ├── .eslintignore ├── .eslintrc.js ├── .github └── workflows │ ├── branch.yml │ ├── eslint.yml │ ├── pypi_deploy.yml │ └── pytest.yml ├── .gitignore ├── CONTRIBUTING.md ├── HISTORY.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── hatch_build.py ├── pyproject.toml ├── tests ├── __init__.py ├── data │ ├── iav │ │ ├── mosdepth │ │ │ ├── ERR6359501 │ │ │ │ ├── ERR6359501.Segment_1_PB2.MH201221.per-base.bed.gz │ │ │ │ ├── ERR6359501.Segment_2_PB1.CY147460.per-base.bed.gz │ │ │ │ ├── ERR6359501.Segment_3_PA.CY146806.per-base.bed.gz │ │ │ │ ├── ERR6359501.Segment_4_HA.MH201222.per-base.bed.gz │ │ │ │ ├── ERR6359501.Segment_5_NP.MH085254.per-base.bed.gz │ │ │ │ ├── ERR6359501.Segment_6_NA.EF190976.per-base.bed.gz │ │ │ │ ├── ERR6359501.Segment_7_M.MH085255.per-base.bed.gz │ │ │ │ └── ERR6359501.Segment_8_NS.MH085256.per-base.bed.gz │ │ │ ├── ERR6359502 │ │ │ │ ├── ERR6359502.Segment_1_PB2.MH201221.per-base.bed.gz │ │ │ │ ├── ERR6359502.Segment_2_PB1.CY147460.per-base.bed.gz │ │ │ │ ├── ERR6359502.Segment_3_PA.CY146806.per-base.bed.gz │ │ │ │ ├── ERR6359502.Segment_4_HA.MH201222.per-base.bed.gz │ │ │ │ ├── ERR6359502.Segment_5_NP.MH085254.per-base.bed.gz │ │ │ │ ├── ERR6359502.Segment_6_NA.EF190976.per-base.bed.gz │ │ │ │ ├── ERR6359502.Segment_7_M.MH085255.per-base.bed.gz │ │ │ │ └── ERR6359502.Segment_8_NS.MH085256.per-base.bed.gz │ │ │ ├── ERR6359503 │ │ │ │ ├── ERR6359503.Segment_1_PB2.MH201221.per-base.bed.gz │ │ │ │ ├── ERR6359503.Segment_2_PB1.CY147460.per-base.bed.gz │ │ │ │ ├── ERR6359503.Segment_3_PA.CY146806.per-base.bed.gz │ │ │ │ ├── ERR6359503.Segment_4_HA.MH201222.per-base.bed.gz │ │ │ │ ├── ERR6359503.Segment_5_NP.MH085254.per-base.bed.gz │ │ │ │ ├── ERR6359503.Segment_6_NA.EF190976.per-base.bed.gz │ │ │ │ ├── ERR6359503.Segment_7_M.MH085255.per-base.bed.gz │ │ │ │ └── ERR6359503.Segment_8_NS.MH085256.per-base.bed.gz │ │ │ └── ERR6359504 │ │ │ │ ├── ERR6359504.Segment_1_PB2.MH201221.per-base.bed.gz │ │ │ │ ├── ERR6359504.Segment_2_PB1.CY147460.per-base.bed.gz │ │ │ │ ├── ERR6359504.Segment_3_PA.CY146806.per-base.bed.gz │ │ │ │ ├── ERR6359504.Segment_4_HA.MH201222.per-base.bed.gz │ │ │ │ ├── ERR6359504.Segment_5_NP.MH085254.per-base.bed.gz │ │ │ │ ├── ERR6359504.Segment_6_NA.EF190976.per-base.bed.gz │ │ │ │ ├── ERR6359504.Segment_7_M.MH085255.per-base.bed.gz │ │ │ │ └── ERR6359504.Segment_8_NS.MH085256.per-base.bed.gz │ │ ├── reference_sequences │ │ │ ├── ERR6359501 │ │ │ │ ├── ERR6359501.Segment_1_PB2.MH201221.reference.fasta │ │ │ │ ├── ERR6359501.Segment_2_PB1.CY147460.reference.fasta │ │ │ │ ├── ERR6359501.Segment_3_PA.CY146806.reference.fasta │ │ │ │ ├── ERR6359501.Segment_4_HA.MH201222.reference.fasta │ │ │ │ ├── ERR6359501.Segment_5_NP.MH085254.reference.fasta │ │ │ │ ├── ERR6359501.Segment_6_NA.EF190976.reference.fasta │ │ │ │ ├── ERR6359501.Segment_7_M.MH085255.reference.fasta │ │ │ │ ├── ERR6359501.Segment_8_NS.MH085256.reference.fasta │ │ │ │ └── ERR6359501.topsegments.csv │ │ │ ├── ERR6359502 │ │ │ │ ├── ERR6359502.Segment_1_PB2.MH201221.reference.fasta │ │ │ │ ├── ERR6359502.Segment_2_PB1.CY147460.reference.fasta │ │ │ │ ├── ERR6359502.Segment_3_PA.CY146806.reference.fasta │ │ │ │ ├── ERR6359502.Segment_4_HA.MH201222.reference.fasta │ │ │ │ ├── ERR6359502.Segment_5_NP.MH085254.reference.fasta │ │ │ │ ├── ERR6359502.Segment_6_NA.EF190976.reference.fasta │ │ │ │ ├── ERR6359502.Segment_7_M.MH085255.reference.fasta │ │ │ │ ├── ERR6359502.Segment_8_NS.MH085256.reference.fasta │ │ │ │ └── ERR6359502.topsegments.csv │ │ │ ├── ERR6359503 │ │ │ │ ├── ERR6359503.Segment_1_PB2.MH201221.reference.fasta │ │ │ │ ├── ERR6359503.Segment_2_PB1.CY147460.reference.fasta │ │ │ │ ├── ERR6359503.Segment_3_PA.CY146806.reference.fasta │ │ │ │ ├── ERR6359503.Segment_4_HA.MH201222.reference.fasta │ │ │ │ ├── ERR6359503.Segment_5_NP.MH085254.reference.fasta │ │ │ │ ├── ERR6359503.Segment_6_NA.EF190976.reference.fasta │ │ │ │ ├── ERR6359503.Segment_7_M.MH085255.reference.fasta │ │ │ │ ├── ERR6359503.Segment_8_NS.MH085256.reference.fasta │ │ │ │ └── ERR6359503.topsegments.csv │ │ │ └── ERR6359504 │ │ │ │ ├── ERR6359504.Segment_1_PB2.MH201221.reference.fasta │ │ │ │ ├── ERR6359504.Segment_2_PB1.CY147460.reference.fasta │ │ │ │ ├── ERR6359504.Segment_3_PA.CY146806.reference.fasta │ │ │ │ ├── ERR6359504.Segment_4_HA.MH201222.reference.fasta │ │ │ │ ├── ERR6359504.Segment_5_NP.MH085254.reference.fasta │ │ │ │ ├── ERR6359504.Segment_6_NA.EF190976.reference.fasta │ │ │ │ ├── ERR6359504.Segment_7_M.MH085255.reference.fasta │ │ │ │ ├── ERR6359504.Segment_8_NS.MH085256.reference.fasta │ │ │ │ └── ERR6359504.topsegments.csv │ │ └── variants │ │ │ ├── ERR6359501 │ │ │ ├── ERR6359501.Segment_1_PB2.MH201221.no_frameshifts.vcf │ │ │ ├── ERR6359501.Segment_2_PB1.CY147460.no_frameshifts.vcf │ │ │ ├── ERR6359501.Segment_3_PA.CY146806.no_frameshifts.vcf │ │ │ ├── ERR6359501.Segment_4_HA.MH201222.no_frameshifts.vcf │ │ │ ├── ERR6359501.Segment_5_NP.MH085254.no_frameshifts.vcf │ │ │ ├── ERR6359501.Segment_6_NA.EF190976.no_frameshifts.vcf │ │ │ ├── ERR6359501.Segment_7_M.MH085255.no_frameshifts.vcf │ │ │ └── ERR6359501.Segment_8_NS.MH085256.no_frameshifts.vcf │ │ │ ├── ERR6359502 │ │ │ ├── ERR6359502.Segment_1_PB2.MH201221.no_frameshifts.vcf │ │ │ ├── ERR6359502.Segment_2_PB1.CY147460.no_frameshifts.vcf │ │ │ ├── ERR6359502.Segment_3_PA.CY146806.no_frameshifts.vcf │ │ │ ├── ERR6359502.Segment_4_HA.MH201222.no_frameshifts.vcf │ │ │ ├── ERR6359502.Segment_5_NP.MH085254.no_frameshifts.vcf │ │ │ ├── ERR6359502.Segment_6_NA.EF190976.no_frameshifts.vcf │ │ │ ├── ERR6359502.Segment_7_M.MH085255.no_frameshifts.vcf │ │ │ └── ERR6359502.Segment_8_NS.MH085256.no_frameshifts.vcf │ │ │ ├── ERR6359503 │ │ │ ├── ERR6359503.Segment_1_PB2.MH201221.no_frameshifts.vcf │ │ │ ├── ERR6359503.Segment_2_PB1.CY147460.no_frameshifts.vcf │ │ │ ├── ERR6359503.Segment_3_PA.CY146806.no_frameshifts.vcf │ │ │ ├── ERR6359503.Segment_4_HA.MH201222.no_frameshifts.vcf │ │ │ ├── ERR6359503.Segment_5_NP.MH085254.no_frameshifts.vcf │ │ │ ├── ERR6359503.Segment_6_NA.EF190976.no_frameshifts.vcf │ │ │ ├── ERR6359503.Segment_7_M.MH085255.no_frameshifts.vcf │ │ │ └── ERR6359503.Segment_8_NS.MH085256.no_frameshifts.vcf │ │ │ └── ERR6359504 │ │ │ ├── ERR6359504.Segment_1_PB2.MH201221.no_frameshifts.vcf │ │ │ ├── ERR6359504.Segment_2_PB1.CY147460.no_frameshifts.vcf │ │ │ ├── ERR6359504.Segment_3_PA.CY146806.no_frameshifts.vcf │ │ │ ├── ERR6359504.Segment_4_HA.MH201222.no_frameshifts.vcf │ │ │ ├── ERR6359504.Segment_5_NP.MH085254.no_frameshifts.vcf │ │ │ ├── ERR6359504.Segment_6_NA.EF190976.no_frameshifts.vcf │ │ │ ├── ERR6359504.Segment_7_M.MH085255.no_frameshifts.vcf │ │ │ └── ERR6359504.Segment_8_NS.MH085256.no_frameshifts.vcf │ └── sars-cov-2 │ │ ├── MN908947.3.fasta │ │ ├── MN908947.3.gff │ │ ├── mosdepth │ │ ├── Sample1.per-base.bed.gz │ │ ├── Sample2.per-base.bed.gz │ │ └── Sample3.per-base.bed.gz │ │ ├── sequence_sars_cov2.gb │ │ └── variants │ │ ├── ivar │ │ ├── Sample3.snpsift.txt │ │ └── Sample3.vcf.gz │ │ └── nanopolish │ │ ├── Sample1.pass.vcf.gz │ │ ├── Sample1.snpsift.txt │ │ ├── Sample2.pass.vcf.gz │ │ └── Sample2.snpsift.txt ├── test_cli.py └── test_io.py ├── web ├── .gitignore ├── README.md ├── data │ ├── flu-db.js │ └── sars-cov-2-db.js ├── index.html ├── package-lock.json ├── package.json ├── postcss.config.js ├── src │ ├── App.tsx │ ├── chartOptions │ │ ├── axes.ts │ │ ├── chartGrid.ts │ │ ├── chartSeries.ts │ │ ├── dataZoom.ts │ │ ├── dataset.ts │ │ ├── depthSeries.ts │ │ ├── geneFeatures.tsx │ │ ├── segmented │ │ │ ├── getSegmentsInfo.ts │ │ │ ├── pcr.ts │ │ │ └── variantSeries.ts │ │ ├── tooltips.ts │ │ ├── variantHeatmap.ts │ │ └── variantSeries.ts │ ├── db.tsx │ ├── index.css │ ├── index.tsx │ ├── state.tsx │ ├── stats.ts │ ├── ui │ │ ├── AboutPage.tsx │ │ ├── ChartContainer.tsx │ │ ├── ChartTooltip.tsx │ │ ├── Nav.tsx │ │ ├── Sidebar.tsx │ │ ├── SummaryInfoPage.tsx │ │ ├── ThemeButton.tsx │ │ ├── components │ │ │ ├── HelpIcon.tsx │ │ │ ├── Slider.tsx │ │ │ └── TooltipTable.tsx │ │ └── sidebar │ │ │ ├── AxisOptionsPanel.tsx │ │ │ ├── ChartDarkModeToggle.tsx │ │ │ ├── CollapseSidebarButton.tsx │ │ │ ├── CollapsiblePanel.tsx │ │ │ ├── ColourOptionsPanel.tsx │ │ │ ├── CovColour.tsx │ │ │ ├── CovPlotYMax.tsx │ │ │ ├── CovPlotYScale.tsx │ │ │ ├── DisplayOptionsPanel.tsx │ │ │ ├── LowCovColour.tsx │ │ │ ├── LowCovRegionsOptions.tsx │ │ │ ├── LowCovThreshold.tsx │ │ │ ├── LowCovThresholdLine.tsx │ │ │ ├── MutationOptionsPanel.tsx │ │ │ ├── NuclColourSelect.tsx │ │ │ ├── SampleSelect.tsx │ │ │ ├── SegmentSelect.tsx │ │ │ ├── SelectEChartsRenderer.tsx │ │ │ ├── ToggleLowCoverageHighlight.tsx │ │ │ ├── TooltipOptionsPanel.tsx │ │ │ └── TooltipTriggerSelect.tsx │ └── util.ts ├── tailwind.config.js ├── tsconfig.json ├── vite.config.build.ts ├── vite.config.flu.ts ├── vite.config.ts └── wgscovplot.html.j2 └── wgscovplot ├── __about__.py ├── __init__.py ├── cli.py ├── colors.py ├── config.py ├── db.py ├── 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