Migrating a v4 config

JBrowse v5 opens a v4.3.0 config.json or saved session unedited. As the file loads, the app rewrites each retired key into the slot that replaced it. The table below lists every key the app rewrites, and a script generates it by running each rewrite.

In: a v4.3.0 key on an adapter, track, display or view
Out: the v5 slot that key becomes, or dropped where v5 reads the key and discards it

jbrowse validate warns on each of these keys in a file, and fails on a key it does not know.

(session) marks a key a saved session wrote on a display or view. The session migration writes it into the track's config, or onto the view.
A type row is a v4 display type. It loads as the display named, with the settings listed.
A dotted path is a nested slot: pileup.mark.height is { "pileup": { "mark": { "height": 7 } } }.
"on LinearSyntenyView" means the setting moves from the display to the view.

Type	v4.3.0 key	v5
`BamAdapter`	`chunkSizeLimit`	dropped
`BamAdapter`, `CramAdapter`, `HtsgetBamAdapter`	`sequenceAdapter`	dropped
`CytobandAdapter`	`cytobandsLocation`	`cytobandLocation`
`FromConfigAdapter`, `FromConfigRegionsAdapter`, `FromConfigSequenceAdapter`	`featureClass`	dropped
`GCContentAdapter`	`windowDelta`	`step`
	`windowSize`	`window`
`HicAdapter`	`resolutionMultiplier`	dropped
`MCScanAnchorsAdapter`	`subadapters`	dropped
`NcbiSequenceReportAliasAdapter`	`useUcscNameOverride`	`useNameOverride`
`JBrowse1TextSearchAdapter`, `TrixTextSearchAdapter`	`tracks`	dropped
`TrixTextSearchAdapter`	`metaFilePath`, `textSearchAdapterId`	dropped
Every track	`rpcDriverName`	dropped
Every track but `ReferenceSequenceTrack`	`textSearchAdapter`	`textSearching.textSearchAdapter`
	`textSearchIndexingAttributes`	`textSearching.indexingAttributes`
`ReferenceSequenceTrack`	`rendering`	dropped
	type `LinearGCContentDisplay`, type `LinearGCContentTrackDisplay`, type `MultiLinearWiggleDisplay`	dropped
`SyntenyTrack`	`trackIds`	dropped
Every display but `ChordSyntenyDisplay`, `ChordVariantDisplay`, `DotplotDisplay`, `LinearBasicDisplay`, `LinearReferenceSequenceDisplay`, `LinearSyntenyDisplay`, `LinearVariantDisplay`	`maxFeatureScreenDensity`, `mouseover`	dropped
Every display but `ChordSyntenyDisplay`, `ChordVariantDisplay`, `DotplotDisplay`, `LinearReferenceSequenceDisplay`, `LinearSyntenyDisplay`	`maxDisplayedBpPerPx`	dropped
Every display but `ChordSyntenyDisplay`, `ChordVariantDisplay`, `DotplotDisplay`, `LinearSyntenyDisplay`	`heightPreConfig` (session)	`height`
`ChordSyntenyDisplay`, `ChordVariantDisplay`, `DotplotDisplay`, `LinearSyntenyDisplay`	`heightPreConfig` (session)	dropped
`ChordVariantDisplay`	`strokeColor`	`encoding.color.value`
	`strokeColorHover`, `strokeColorSelected`	dropped
`ChordVariantDisplay`, `LinearVariantDisplay`	`renderer`	`encoding.color.value`
`DotplotDisplay`	`alpha` (session)	`encoding.opacity` on `DotplotView`
	`colorBy` (session)	`encoding.color.field` on `DotplotView`
	`minAlignmentLength` (session)	`filter` on `DotplotView`
`DotplotDisplay`, `LinearHicDisplay`, `LinearReferenceSequenceDisplay`, `LinearSyntenyDisplay`	`renderer`	dropped
`LDTrackDisplay`	`fitToHeight`	`heightMode`
	`ldMetric`	`encoding.color.field`
	`lineZoneHeight`	`connectors.height`
	`showLegend`	`legend.show`
	`showVerticalGuides`	`guides.show`
	`useGenomicPositions`	`variantLayout`
	`callRateFilter`, `hweFilterThreshold`, `lengthCutoffFilter`, `minorAlleleFrequencyFilter`, `recombinationZoneHeight`, `showLDTriangle`, `showRecombination`, `signedLD`	dropped
`LDTrackDisplay`, `LGVSyntenyDisplay`, `LinearAlignmentsDisplay`	`colorScheme`	dropped
`LDTrackDisplay`, `LGVSyntenyDisplay`, `LinearAlignmentsDisplay`, `LinearMafDisplay`, `LinearWiggleDisplay`, `MultiWaySyntenyDisplay`	`jexlFilters`	dropped
`LDTrackDisplay`, `LinearBasicDisplay`	`showLabels`	`labels.name.show`
`LDTrackDisplay`, `LinearBasicDisplay`, `LinearVariantDisplay`	`maxHeight`	dropped
`LGVSyntenyDisplay`	`colorBy`	`encoding.color.field`
`LGVSyntenyDisplay`, `LinearAlignmentsDisplay`	`autoscale`	`coverage.encoding.y.scale.fenceQuantile`
	`featureHeight`	`pileup.mark.height`
	`hideMismatches`	`pileup.mismatches.show`
	`lineWidth`	`readConnections.encoding.strokeWidth.value`
	`maxHeight`	`pileup.maxLayoutHeight`
	`maxScore`	`coverage.encoding.y.scale.domainMax`
	`minScore`	`coverage.encoding.y.scale.domainMin`
	`mismatchAlpha`	`pileup.mismatches.encoding.opacity.field`
	`pileupDisplay`	`pileup.mark.height`, `pileup.maxLayoutHeight`
	`renderers`	`pileup.mark.height`, `pileup.maxLayoutHeight`, `pileup.mismatches.encoding.opacity.field`, `pileup.mismatches.show`
	`scaleType`	`coverage.encoding.y.scale.type`
	`snpCoverageDisplay`	`coverage.encoding.y.scale.domainMin`, `coverage.height`
	`defaultRendering`, `hideLargeIndels`, `hideSmallIndels`, `jitter`, `minSubfeatureWidth`, `multiTicks`	dropped
`LGVSyntenyDisplay`, `LinearAlignmentsDisplay`, `LinearVariantDisplay`, `LinearWiggleDisplay`	`inverted`, `numStdDev`	dropped
`LinearAlignmentsDisplay`	`colorBy`	`encoding.color.field`, `pileup.bases.encoding.color.field`, `pileup.bases.show`
	type `LinearPileupDisplay`	`LinearAlignmentsDisplay` with `coverage.show: false`, `sashimi.show: false`
	type `LinearReadArcsDisplay`	`LinearAlignmentsDisplay` with `pileup.show: false`, `coverage.show: false`, `sashimi.show: false`, `readConnections.show: true`
	type `LinearReadCloudDisplay`	`LinearAlignmentsDisplay` with `pileup.show: false`, `coverage.show: false`, `sashimi.show: false`, `readConnections.show: true`, `readConnections.mark: "rule"`
	type `LinearSNPCoverageDisplay`	`LinearAlignmentsDisplay` with `pileup.show: false`, `coverage.height: 100`, `height: 100`
	`autoscale` (session)	`coverage.encoding.y.scale.fenceQuantile`
	`colorBy` (session), `colorBySetting` (session)	`encoding.color.field`, `pileup.bases.encoding.color.field`, `pileup.bases.show`
	`constraints` (session)	`coverage.encoding.y.scale.domainMax`, `coverage.encoding.y.scale.domainMin`
	`displayCrossHatches` (session)	`coverage.encoding.y.axis.grid`
	`drawProperPairs` (session)	`readConnections.ordinaryPairs.show`
	`drawSingletons` (session), `filterBy` (session), `filterBySetting` (session)	`filter`
	`hideMismatchesSetting` (session)	`pileup.mismatches.show`
	`PileupDisplay` (session)	`encoding.color.field`, `pileup.maxLayoutHeight`
	`scale` (session)	`coverage.encoding.y.scale.type`
	`SNPCoverageDisplay` (session)	`coverage.encoding.y.axis.grid`, `coverage.encoding.y.scale.type`
	`snpCovHeight` (session)	`coverage.height`
	`sortedBy` (session)	`sort.field`, `sort.pos`, `sort.refName`
	`trackMaxHeight` (session)	`pileup.maxLayoutHeight`
`LinearAlignmentsDisplay`, `LinearHicDisplay`	`showLegend` (session)	`legend.show`
`LinearArcDisplay`	`color`, `renderer`	dropped
`LinearBasicDisplay`	`color3`	`utrs.encoding.color.value`
	`containerTypes`	`containers.types`
	`displayMode: "collapse"`, `displayMode: "reducedRepresentation"`	`displayMode: "normal"`
	`featureHeight`	`mark.height`
	`geneGlyphMode: "longest"`, `geneGlyphMode: "longestCoding"`	`geneGlyphMode: "representative"`
	`mouseover`	`tooltip.field`
	`renderer`	`encoding.color.value`, `utrs.encoding.color.value`
	`showDescriptions`	`labels.description.show`
	`subfeatureLabels`	`labels.subfeatures.placement`, `labels.subfeatures.show`
	`transcriptTypes`	`transcripts.types`
	type `LinearFeatureDisplay`	`LinearBasicDisplay`
	`color2`, `impliedUTRs`, `outline`	dropped
	`trackDisplayMode` (session)	`displayMode`
`LinearBasicDisplay`, `LinearHicDisplay`, `LinearManhattanDisplay`, `LinearMarkDisplay`, `LinearMultiRowFeatureDisplay`, `LinearVariantDisplay`	`jexlFilters`	`filter`
`LinearBasicDisplay`, `LinearVariantDisplay`	`color1`	`encoding.color.value`
	`jexlFiltersSetting` (session)	`filter`
`LinearHicDisplay`	`activeNormalization` (session)	`data.normalization`
	`colorScheme` (session)	`encoding.color.scale.reverse`, `encoding.color.scale.scheme`
	`useLogScale` (session)	`encoding.color.scale.type`
	`mode` (session)	dropped
`LinearHicDisplay`, `LinearWiggleDisplay`	`fetchSizeLimit`	dropped
	`resolution` (session)	`data.resolution`
`LinearMafDisplay`	`rowHeight`	dropped
`LinearMafDisplay`, `LinearVariantDisplay`, `LinearWiggleDisplay`	`subtreeFilter` (session)	`rows.kept`
	`treeAreaWidth` (session)	`rows.axis.width`
`LinearMarkDisplay`	type `LinearArcDisplay`	`LinearMarkDisplay` with `marks: [{"mark":"link"}]`
	type `LinearPairedArcDisplay`	`LinearMarkDisplay` with `marks: [{"mark":"link","transform":[{"type":"mate"}],"encoding":{"x2":{"refName":"mate.refName","pos":"mate.start"}}}]`
`LinearPairedArcDisplay`	`color`, `renderer`	dropped
`LinearSyntenyDisplay`	`middle`	dropped
	`alpha` (session)	`encoding.opacity` on `LinearSyntenyView`
	`colorBy` (session)	`encoding.color.field` on `LinearSyntenyView`
	`minAlignmentLength` (session)	`filter` on `LinearSyntenyView`
`LinearVariantDisplay`	`colorBy`	`rows.color`
	`featureHeight`	`records.mark.height`
	`maxFeatureScreenDensity`	`records.maxFeatureScreenDensity`
	`minorAlleleFrequencyFilter`	`filter`
	`mouseover`	`records.tooltip.field`
	`renderingMode`	`rows.field`
	`showDescriptions`	`records.labels.description.show`
	`showLabels`	`records.labels.name.show`
	`referenceDrawingMode`, `showReferenceAlleles`	`genotypes.reference.show`
	`showSidebarLabels`	`rows.axis.labels`
	`showTree`	`rows.axis.tree`
	type `LinearMultiSampleVariantDisplay`, type `MultiLinearVariantDisplay`	`LinearVariantDisplay`
	type `LinearVariantMatrixDisplay`	`LinearVariantDisplay` with `variantLayout: "columns"`
	`autoscale`, `maxScore`, `minScore`, `scaleType`	dropped
	`jexlFilters` (session)	`filter`
	`layout` (session)	`rows.sort`
	`lineZoneHeight` (session)	`connectors.height`
	`referenceDrawingModeSetting` (session)	`genotypes.reference.show`
	`renderingModeSetting` (session)	`rows.field`
	`rowHeightMode` (session)	`rows.step`
	`minorAlleleFrequencyFilterSetting` (session)	dropped
`LinearVariantDisplay`, `LinearWiggleDisplay`	`minimalTicks`	dropped
	`clusterTree` (session)	`rows.tree`
	`showSidebarLabelsSetting` (session)	`rows.axis.labels`
	`showTreeSetting` (session)	`rows.axis.tree`
`LinearWiggleDisplay`	`autoscale`	`encoding.y.scale.fenceQuantile`
	`defaultRendering`	`mark.interpolate`, `mark.type`
	`displayCrossHatches`	`encoding.y.axis.grid`
	`maxScore`	`encoding.y.scale.domainMax`
	`minScore`	`encoding.y.scale.domainMin`
	`renderers`	`encoding.color.value`, `encoding.y.field`, `mark.extent`
	`scaleType`	`encoding.y.scale.type`
	type `LinearGCContentDisplay`, type `LinearGCContentTrackDisplay`, type `MultiLinearWiggleDisplay`	`LinearWiggleDisplay`
	`autoscale` (session)	`encoding.y.scale.fenceQuantile`
	`color` (session)	`encoding.color.value`
	`constraints` (session)	`encoding.y.scale.domainMax`, `encoding.y.scale.domainMin`
	`displayCrossHatches` (session)	`encoding.y.axis.grid`
	`layout` (session)	`rows.colors`, `rows.sort`
	`negColor` (session), `posColor` (session)	`encoding.color.scale.range`
	`rendererTypeNameState` (session)	`mark.type`
	`scale` (session)	`encoding.y.scale.type`
	`summaryScoreMode` (session)	`encoding.y.field`, `mark.extent`
`MultiLinearWiggleDisplay`	`defaultRendering`	`mark.interpolate`, `mark.type`, `rows.field` on `LinearWiggleDisplay`
`DotplotView`	`alpha` (session)	`encoding.opacity`
	`colorBy` (session)	`encoding.color.field`
	`drawCigar` (session)	`indels.show`
`LinearSyntenyView`	`alpha` (session)	`encoding.opacity`
	`colorBy` (session)	`encoding.color.field`
	`drawCigar` (session)	`indels.show`
	`tracks` (session)	`levels[0].tracks`