@jbrowse/launch-args 5.0.0-beta.17 → 5.0.0-beta.19

package/esm/displaySlots.generated.js

@@ -0,0 +1,23 @@
+// Generated by scripts/generateDisplaySlots.ts from the committed config
+// schema — do not edit by hand. Regenerate with `pnpm autogen`.
+/** Each display type's config slot paths, three segments deep, a list's members under its name. */
+export const displaySlotPaths = {
+    ChordSyntenyDisplay: ["displayId", "mark", "mark.depth", "type"],
+    ChordVariantDisplay: ["displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "encoding.opacity", "encoding.opacity.value", "mark", "mark.depth", "onChordClick", "renderer", "strokeColor", "strokeColorHover", "strokeColorSelected", "type"],
+    DotplotDisplay: ["displayId", "renderer", "type"],
+    LDTrackDisplay: ["callRateFilter", "colorScheme", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "fetchSizeLimit", "fitToHeight", "guides", "guides.show", "height", "heightMode", "hweFilterThreshold", "jexlFilters", "labels", "labels.name", "labels.name.show", "ldMetric", "legend", "legend.show", "lengthCutoffFilter", "lineZoneHeight", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "maxHeight", "minorAlleleFrequencyFilter", "mouseover", "recombinationZoneHeight", "showLDTriangle", "showLabels", "showLegend", "showRecombination", "showVerticalGuides", "signedLD", "tickHeight", "type", "useGenomicPositions", "variantLayout"],
+    LGVSyntenyDisplay: ["autoscale", "collapseSections", "colorBy", "colorScheme", "coverage", "coverage.alleles", "coverage.alleles.filter", "coverage.alleles.show", "coverage.encoding", "coverage.encoding.y", "coverage.height", "coverage.interbase", "coverage.interbase.filter", "coverage.interbase.show", "coverage.show", "data", "data.resolution", "defaultRendering", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "facet", "facet.field", "facet.hidden", "facet.sort", "featureHeight", "fetchSizeLimit", "filter", "filter.equal", "filter.field", "filter.gt", "filter.gte", "filter.lt", "filter.lte", "filter.oneOf", "filter.range", "filter.valid", "forceLoad", "growMaxHeight", "height", "heightMode", "hideLargeIndels", "hideMismatches", "hideSmallIndels", "inverted", "jexlFilters", "jitter", "legend", "legend.show", "lineWidth", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "maxHeight", "maxScore", "minScore", "minSubfeatureWidth", "mismatchAlpha", "mouseover", "multiTicks", "numStdDev", "pileup", "pileup.connectors", "pileup.connectors.show", "pileup.fadeLowFrequency", "pileup.mark", "pileup.mark.height", "pileup.maxLayoutHeight", "pileup.mismatches", "pileup.mismatches.encoding", "pileup.mismatches.show", "pileup.show", "pileup.softClips", "pileup.softClips.show", "pileupDisplay", "readConnections", "readConnections.encoding", "readConnections.encoding.color", "readConnections.encoding.strokeWidth", "readConnections.height", "readConnections.mark", "readConnections.mark.type", "readConnections.ordinaryPairs", "readConnections.ordinaryPairs.show", "readConnections.placement", "readConnections.show", "renderers", "scaleType", "snpCoverageDisplay", "sort", "sort.field", "sort.pos", "sort.refName", "sort.within", "type", "unit"],
+    LinearAlignmentsDisplay: ["autoscale", "collapseSections", "colorBy", "colorScheme", "coverage", "coverage.alleles", "coverage.alleles.filter", "coverage.alleles.show", "coverage.encoding", "coverage.encoding.y", "coverage.height", "coverage.interbase", "coverage.interbase.filter", "coverage.interbase.show", "coverage.show", "defaultRendering", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "facet", "facet.field", "facet.hidden", "facet.sort", "featureHeight", "fetchSizeLimit", "filter", "filter.equal", "filter.field", "filter.gt", "filter.gte", "filter.lt", "filter.lte", "filter.oneOf", "filter.range", "filter.valid", "forceLoad", "growMaxHeight", "height", "heightMode", "hideLargeIndels", "hideMismatches", "hideSmallIndels", "inverted", "jexlFilters", "jitter", "legend", "legend.show", "lineWidth", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "maxHeight", "maxScore", "minScore", "minSubfeatureWidth", "mismatchAlpha", "mouseover", "multiTicks", "numStdDev", "pileup", "pileup.bases", "pileup.bases.encoding", "pileup.bases.filter", "pileup.bases.show", "pileup.bases.unmodified", "pileup.connectors", "pileup.connectors.show", "pileup.fadeLowFrequency", "pileup.mark", "pileup.mark.height", "pileup.maxLayoutHeight", "pileup.mismatches", "pileup.mismatches.encoding", "pileup.mismatches.show", "pileup.show", "pileup.softClips", "pileup.softClips.show", "pileupDisplay", "readConnections", "readConnections.encoding", "readConnections.encoding.color", "readConnections.encoding.strokeWidth", "readConnections.height", "readConnections.mark", "readConnections.mark.type", "readConnections.ordinaryPairs", "readConnections.ordinaryPairs.show", "readConnections.placement", "readConnections.show", "renderers", "sashimi", "sashimi.height", "sashimi.labels", "sashimi.labels.show", "sashimi.placement", "sashimi.show", "scaleType", "snpCoverageDisplay", "sort", "sort.field", "sort.pos", "sort.refName", "sort.within", "type", "unit"],
+    LinearBasicDisplay: ["chevrons", "chevrons.show", "color1", "color2", "color3", "containerTypes", "containers", "containers.types", "displayId", "displayMode", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "facet", "facet.field", "facet.hidden", "facet.sort", "featureHeight", "fetchSizeLimit", "filter", "filter.equal", "filter.field", "filter.gt", "filter.gte", "filter.lt", "filter.lte", "filter.oneOf", "filter.range", "filter.valid", "forceLoad", "geneGlyphMode", "growMaxHeight", "height", "heightMode", "impliedUTRs", "jexlFilters", "labels", "labels.description", "labels.description.field", "labels.description.show", "labels.name", "labels.name.field", "labels.name.show", "labels.subfeatures", "labels.subfeatures.placement", "labels.subfeatures.show", "legend", "legend.show", "mark", "mark.height", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "maxHeight", "mouseover", "outline", "renderer", "showDescriptions", "showLabels", "subfeatureLabels", "tooltip", "tooltip.field", "tooltip.show", "transcriptTypes", "transcripts", "transcripts.field", "transcripts.sort", "transcripts.types", "type", "utrs", "utrs.encoding", "utrs.encoding.color"],
+    LinearHicDisplay: ["data", "data.normalization", "data.resolution", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "fetchSizeLimit", "filter", "filter.equal", "filter.field", "filter.gt", "filter.gte", "filter.lt", "filter.lte", "filter.oneOf", "filter.range", "filter.valid", "height", "heightMode", "jexlFilters", "legend", "legend.show", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "mouseover", "renderer", "type"],
+    LinearMafDisplay: ["alignments", "alignments.bases", "alignments.bases.encoding", "alignments.bases.show", "alignments.frames", "alignments.frames.show", "alignments.inversions", "alignments.inversions.show", "alignments.mismatches", "alignments.mismatches.show", "alignments.reference", "alignments.reference.show", "alignments.rowProportion", "alignments.show", "axis", "axis.branchLength", "axis.labels", "axis.tree", "axis.width", "conservation", "conservation.height", "conservation.show", "conservation.unit", "coverage", "coverage.alleles", "coverage.alleles.filter", "coverage.alleles.show", "coverage.encoding", "coverage.encoding.y", "coverage.height", "coverage.interbase", "coverage.interbase.filter", "coverage.interbase.show", "coverage.show", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "encoding.y", "encoding.y.field", "fetchSizeLimit", "forceLoad", "height", "jexlFilters", "legend", "legend.show", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "mouseover", "rowColor", "rowColor.field", "rowColor.scale", "rowColor.scale.domain", "rowColor.scale.range", "rowColor.scale.unknown", "rowHeight", "rows", "rows.field", "rows.kept", "rows.labels", "rows.sort", "rows.tree", "rows.treeProvenance", "type"],
+    LinearManhattanDisplay: ["axis", "axis.branchLength", "axis.grid", "axis.labels", "axis.tree", "axis.width", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "encoding.y", "encoding.y.axis", "encoding.y.rules", "encoding.y.scale", "facet", "facet.field", "facet.hidden", "facet.sort", "facet.transform", "facet.transform.as", "facet.transform.expr", "facet.transform.field", "facet.transform.fields", "facet.transform.frame", "facet.transform.groupby", "facet.transform.index", "facet.transform.keepEmpty", "facet.transform.key", "facet.transform.ops", "facet.transform.padding", "facet.transform.step", "facet.transform.type", "fetchSizeLimit", "filter", "filter.equal", "filter.field", "filter.gt", "filter.gte", "filter.lt", "filter.lte", "filter.oneOf", "filter.range", "filter.valid", "forceLoad", "height", "jexlFilters", "legend", "legend.show", "marks", "marks.encoding", "marks.encoding.color", "marks.encoding.row", "marks.encoding.shape", "marks.encoding.size", "marks.encoding.strokeWidth", "marks.encoding.text", "marks.encoding.x", "marks.encoding.x2", "marks.encoding.y", "marks.mark", "marks.mark.gapBp", "marks.mark.height", "marks.mark.interpolate", "marks.mark.type", "marks.maxBpPerPx", "marks.minBpPerPx", "marks.transform", "marks.transform.as", "marks.transform.expr", "marks.transform.field", "marks.transform.fields", "marks.transform.frame", "marks.transform.groupby", "marks.transform.index", "marks.transform.keepEmpty", "marks.transform.key", "marks.transform.ops", "marks.transform.padding", "marks.transform.step", "marks.transform.type", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "mouseover", "origin", "rowColor", "rowColor.field", "rowColor.scale", "rowColor.scale.domain", "rowColor.scale.range", "rowColor.scale.unknown", "rowGroups", "rowGroups.group", "rowGroups.match", "rowHeight", "rows", "rows.field", "rows.kept", "rows.labels", "rows.sort", "rows.tree", "rows.treeProvenance", "transform", "transform.as", "transform.expr", "transform.field", "transform.fields", "transform.frame", "transform.groupby", "transform.index", "transform.keepEmpty", "transform.key", "transform.ops", "transform.ops.as", "transform.ops.field", "transform.ops.op", "transform.ops.weight", "transform.padding", "transform.step", "transform.type", "type"],
+    LinearMarkDisplay: ["axis", "axis.branchLength", "axis.grid", "axis.labels", "axis.tree", "axis.width", "color", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "encoding.y", "encoding.y.axis", "encoding.y.rules", "encoding.y.scale", "facet", "facet.field", "facet.hidden", "facet.sort", "facet.transform", "facet.transform.as", "facet.transform.expr", "facet.transform.field", "facet.transform.fields", "facet.transform.frame", "facet.transform.groupby", "facet.transform.index", "facet.transform.keepEmpty", "facet.transform.key", "facet.transform.ops", "facet.transform.padding", "facet.transform.step", "facet.transform.type", "fetchSizeLimit", "filter", "filter.equal", "filter.field", "filter.gt", "filter.gte", "filter.lt", "filter.lte", "filter.oneOf", "filter.range", "filter.valid", "forceLoad", "height", "jexlFilters", "legend", "legend.show", "marks", "marks.encoding", "marks.encoding.color", "marks.encoding.row", "marks.encoding.shape", "marks.encoding.size", "marks.encoding.strokeWidth", "marks.encoding.text", "marks.encoding.x", "marks.encoding.x2", "marks.encoding.y", "marks.mark", "marks.mark.gapBp", "marks.mark.height", "marks.mark.interpolate", "marks.mark.type", "marks.maxBpPerPx", "marks.minBpPerPx", "marks.transform", "marks.transform.as", "marks.transform.expr", "marks.transform.field", "marks.transform.fields", "marks.transform.frame", "marks.transform.groupby", "marks.transform.index", "marks.transform.keepEmpty", "marks.transform.key", "marks.transform.ops", "marks.transform.padding", "marks.transform.step", "marks.transform.type", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "mouseover", "origin", "renderer", "rowColor", "rowColor.field", "rowColor.scale", "rowColor.scale.domain", "rowColor.scale.range", "rowColor.scale.unknown", "rowGroups", "rowGroups.group", "rowGroups.match", "rowHeight", "rows", "rows.field", "rows.kept", "rows.labels", "rows.sort", "rows.tree", "rows.treeProvenance", "transform", "transform.as", "transform.expr", "transform.field", "transform.fields", "transform.frame", "transform.groupby", "transform.index", "transform.keepEmpty", "transform.key", "transform.ops", "transform.ops.as", "transform.ops.field", "transform.ops.op", "transform.ops.weight", "transform.padding", "transform.step", "transform.type", "type"],
+    LinearMultiRowFeatureDisplay: ["axis", "axis.branchLength", "axis.grid", "axis.labels", "axis.tree", "axis.width", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "encoding.y", "encoding.y.axis", "encoding.y.rules", "encoding.y.scale", "facet", "facet.field", "facet.hidden", "facet.sort", "facet.transform", "facet.transform.as", "facet.transform.expr", "facet.transform.field", "facet.transform.fields", "facet.transform.frame", "facet.transform.groupby", "facet.transform.index", "facet.transform.keepEmpty", "facet.transform.key", "facet.transform.ops", "facet.transform.padding", "facet.transform.step", "facet.transform.type", "fetchSizeLimit", "filter", "filter.equal", "filter.field", "filter.gt", "filter.gte", "filter.lt", "filter.lte", "filter.oneOf", "filter.range", "filter.valid", "forceLoad", "height", "jexlFilters", "legend", "legend.show", "marks", "marks.encoding", "marks.encoding.color", "marks.encoding.row", "marks.encoding.shape", "marks.encoding.size", "marks.encoding.strokeWidth", "marks.encoding.text", "marks.encoding.x", "marks.encoding.x2", "marks.encoding.y", "marks.mark", "marks.mark.gapBp", "marks.mark.height", "marks.mark.interpolate", "marks.mark.type", "marks.maxBpPerPx", "marks.minBpPerPx", "marks.transform", "marks.transform.as", "marks.transform.expr", "marks.transform.field", "marks.transform.fields", "marks.transform.frame", "marks.transform.groupby", "marks.transform.index", "marks.transform.keepEmpty", "marks.transform.key", "marks.transform.ops", "marks.transform.padding", "marks.transform.step", "marks.transform.type", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "mouseover", "origin", "rowColor", "rowColor.field", "rowColor.scale", "rowColor.scale.domain", "rowColor.scale.range", "rowColor.scale.unknown", "rowGroups", "rowGroups.group", "rowGroups.match", "rowHeight", "rows", "rows.field", "rows.kept", "rows.labels", "rows.sort", "rows.tree", "rows.treeProvenance", "transform", "transform.as", "transform.expr", "transform.field", "transform.fields", "transform.frame", "transform.groupby", "transform.index", "transform.keepEmpty", "transform.key", "transform.ops", "transform.ops.as", "transform.ops.field", "transform.ops.op", "transform.ops.weight", "transform.padding", "transform.step", "transform.type", "type"],
+    LinearMultiSampleVariantDisplay: ["autoscale", "axis", "axis.branchLength", "axis.grid", "axis.labels", "axis.tree", "axis.width", "colorBy", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "facet", "facet.field", "facet.sort", "fetchSizeLimit", "filter", "filter.equal", "filter.field", "filter.gt", "filter.gte", "filter.lt", "filter.lte", "filter.oneOf", "filter.range", "filter.valid", "forceLoad", "height", "inverted", "jexlFilters", "legend", "legend.show", "lineZoneHeight", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "maxScore", "minScore", "minimalTicks", "minorAlleleFrequencyFilter", "mouseover", "numStdDev", "referenceDrawingMode", "renderingMode", "rowColor", "rowColor.field", "rowColor.scale", "rowColor.scale.domain", "rowColor.scale.range", "rowColor.scale.unknown", "rowHeight", "rows", "rows.field", "rows.kept", "rows.labels", "rows.sort", "rows.tree", "rows.treeProvenance", "scaleType", "shadeByDosage", "showReferenceAlleles", "showSidebarLabels", "showTree", "tooltip", "tooltip.show", "type", "unit", "variantLayout"],
+    LinearReferenceSequenceDisplay: ["displayId", "fetchSizeLimit", "forceLoad", "forward", "forward.show", "height", "renderer", "reverse", "reverse.show", "translation", "translation.show", "type"],
+    LinearSyntenyDisplay: ["displayId", "middle", "renderer", "type"],
+    LinearVariantDisplay: ["color1", "color2", "color3", "containerTypes", "displayId", "displayMode", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "facet", "facet.field", "facet.hidden", "facet.sort", "featureHeight", "fetchSizeLimit", "filter", "filter.equal", "filter.field", "filter.gt", "filter.gte", "filter.lt", "filter.lte", "filter.oneOf", "filter.range", "filter.valid", "forceLoad", "growMaxHeight", "height", "heightMode", "impliedUTRs", "jexlFilters", "labels", "labels.description", "labels.description.field", "labels.description.show", "labels.name", "labels.name.field", "labels.name.show", "legend", "legend.show", "mark", "mark.height", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "maxHeight", "mouseover", "outline", "renderer", "showDescriptions", "showLabels", "subfeatureLabels", "tooltip", "tooltip.field", "tooltip.show", "transcriptTypes", "type"],
+    LinearWiggleDisplay: ["autoscale", "axis", "axis.branchLength", "axis.grid", "axis.labels", "axis.tree", "axis.width", "data", "data.resolution", "defaultRendering", "displayCrossHatches", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "encoding.size", "encoding.size.value", "encoding.strokeWidth", "encoding.strokeWidth.value", "encoding.y", "encoding.y.axis", "encoding.y.field", "encoding.y.rules", "encoding.y.scale", "fetchSizeLimit", "height", "inverted", "jexlFilters", "legend", "legend.show", "mark", "mark.extent", "mark.interpolate", "mark.type", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "maxScore", "minScore", "minimalTicks", "mouseover", "numStdDev", "origin", "renderers", "rowColor", "rowColor.field", "rowColor.scale", "rowColor.scale.domain", "rowColor.scale.range", "rowColor.scale.unknown", "rows", "rows.field", "rows.kept", "rows.labels", "rows.sort", "rows.tree", "rows.treeProvenance", "scaleType", "type"],
+    MultiWaySyntenyDisplay: ["axis", "axis.show", "data", "data.resolution", "displayId", "encoding", "encoding.color", "encoding.color.field", "encoding.color.legend", "encoding.color.scale", "encoding.color.value", "fetchSizeLimit", "forceLoad", "height", "jexlFilters", "labels", "labels.lanes", "labels.lanes.placement", "labels.name", "labels.name.field", "labels.name.show", "laneGeneTracks", "laneLayers", "laneLayers.adapter", "laneLayers.adapter.baseUri", "laneLayers.adapter.type", "laneLayers.adapter.uri", "laneLayers.height", "laneLayers.marks", "laneLayers.marks.encoding", "laneLayers.marks.mark", "laneLayers.marks.maxBpPerPx", "laneLayers.marks.minBpPerPx", "laneLayers.marks.transform", "laneLayers.name", "laneLayers.tracks", "legend", "legend.show", "maxDisplayedBpPerPx", "maxFeatureScreenDensity", "mouseover", "ribbons", "ribbons.encoding", "ribbons.encoding.color", "ribbons.encoding.opacity", "ribbons.filter", "ribbons.filter.equal", "ribbons.filter.field", "ribbons.filter.gt", "ribbons.filter.gte", "ribbons.filter.lt", "ribbons.filter.lte", "ribbons.filter.oneOf", "ribbons.filter.range", "ribbons.filter.valid", "ribbons.mark", "ribbons.mark.interpolate", "rows", "rows.field", "rows.kept", "rows.labels", "rows.sort", "rows.tree", "rows.treeProvenance", "type", "utrs", "utrs.encoding", "utrs.encoding.color"],
+};

package/esm/fileAdapter.d.ts

@@ -33,6 +33,8 @@ export declare function guessTrack({ location, index, bed1, bed2, adapterType, m
     adapter: Adapter;
     files: (string | undefined)[];
 };
+/** The adapter a file's name says, without looking for its index. */
+export declare function adapterTypeByName(file: string): string | undefined;
 export declare function guessTrackType(adapterType: string, location?: string): string;
 export declare const syntenyAdapterTypes: Set<string>;
 export {};

package/esm/fileAdapter.js

@@ -139,6 +139,11 @@ export function guessTrack({ location, index, bed1, bed2, adapterType, mapLocati
     }
     return { adapter: { type: typeOverride ?? 'UNKNOWN' }, files: [] };
 }
+/** The adapter a file's name says, without looking for its index. */
+export function adapterTypeByName(file) {
+    const spec = matchFormat(fileNameOf(file))?.spec;
+    return spec && 'adapterType' in spec ? spec.adapterType : undefined;
+}
 export function guessTrackType(adapterType, location) {
     return (trackTypeForAdapter(adapterType, location && fileNameOf(location)) ||
         'FeatureTrack');

package/esm/fileInput.d.ts

@@ -13,27 +13,33 @@ export interface Track {
     [key: string]: unknown;
 }
 /**
- * A command-line file as a JBrowse location: a URL (http, s3, ftp, …) is a
- * `uri`, anything else a local path.
+ * A command-line file as a JBrowse location: a URL is a `uri`, anything else a
+ * local path.
  */
 export declare function makeLocation(file: string): Location;
 /**
- * The adapter each typed track flag names. `--bam reads` opens `reads` as BAM
- * whatever its name says, and `--file reads.bam` (or a bare `reads.bam`) types
- * it by name; both build through the add-track format table.
+ * The formats each typed track flag reads, each as the adapters for a plain
+ * file and its bgzipped, tabix-indexed form. `--vcf calls` opens a name that
+ * says none of a flag's formats as its first, `--gff genes.gtf` the format the
+ * name says, and `--bed reads.bam` throws. Both build through the add-track
+ * format table.
  */
-export declare const trackFlagAdapters: {
-    readonly bam: 'BamAdapter';
-    readonly cram: 'CramAdapter';
-    readonly bigwig: 'BigWigAdapter';
-    readonly vcfgz: 'VcfTabixAdapter';
-    readonly gffgz: 'Gff3TabixAdapter';
-    readonly hic: 'HicAdapter';
-    readonly bigbed: 'BigBedAdapter';
-    readonly bedgz: 'BedTabixAdapter';
+export declare const trackFlagFormats: {
+    readonly bam: readonly [readonly ["BamAdapter"]];
+    readonly cram: readonly [readonly ["CramAdapter"]];
+    readonly bigwig: readonly [readonly ["BigWigAdapter"]];
+    readonly bigbed: readonly [readonly ["BigBedAdapter"]];
+    readonly hic: readonly [readonly ["HicAdapter"]];
+    readonly vcf: readonly [readonly ["VcfAdapter", "VcfTabixAdapter"]];
+    readonly gff: readonly [readonly ["Gff3Adapter", "Gff3TabixAdapter"], readonly ["GtfAdapter", "GtfTabixAdapter"]];
+    readonly bed: readonly [readonly ["BedAdapter", "BedTabixAdapter"], readonly ["BedGraphAdapter", "BedGraphTabixAdapter"], readonly ["BedpeAdapter"]];
 };
-export type TrackFlag = keyof typeof trackFlagAdapters;
+export type TrackFlag = keyof typeof trackFlagFormats;
 export declare const trackFlags: TrackFlag[];
+export declare function isTrackFlag(flag: string): flag is TrackFlag;
+/** The flags that open a genome file. */
+export declare const genomeFlags: readonly ['fasta', 'chromSizes'];
+export declare function isGenomeFlag(flag: string): boolean;
 /**
  * The adapter for one file argument: `adapterType`'s when given, else the one
  * its name says. Its index is found beside it unless `index` names one. Throws
@@ -43,7 +49,9 @@ export declare function fileAdapter(file: string, { adapterType, index }?: {
     adapterType?: string;
     index?: string;
 }): Adapter;
-export declare function isSequenceAdapter(adapter: Adapter): boolean;
+export declare function isSequenceAdapter({ type }: {
+    type: string;
+}): boolean;
 /**
  * An assembly from a sequence file's adapter, named after the file, with the
  * `aliases:` and `cytobands:` files a modifier or flag gives it.
@@ -53,6 +61,17 @@ export declare function sequenceAssembly(adapter: Adapter, file: string, { alias
     cytobands?: string;
     trackId?: string;
 }): Assembly;
+/**
+ * The assembly a genome argument opens, `--fasta ref.fa`, `--chromSizes
+ * a.sizes` or a bare genome file, with the files its `aliases:` and
+ * `cytobands:` modifiers name. `--fasta` opens a name the format table does not
+ * know as an indexed FASTA. `unused` is the modifiers it has no use for, for
+ * the caller to report.
+ */
+export declare function genomeAssembly(flag: string, [file, ...mods]: string[], trackId?: string): {
+    assembly: Assembly;
+    unused: string[];
+};
 /**
  * A track for one file argument, labelled by `name:` or the file's basename.
  * Without `assemblyName` it names no assembly, for a caller that learns the

package/esm/fileInput.js

@@ -1,34 +1,65 @@
-import path from 'node:path';
-import { guessTrack, guessTrackType } from './fileAdapter.js';
-import { FILE_FLAG, modifierValue } from './parseArgv.js';
-const URL_SCHEME = /^[a-z][a-z0-9+.-]*:\/\//i;
+import { fileNameOf } from '@jbrowse/add-track-core';
+import { adapterTypeByName, guessTrack, guessTrackType } from './fileAdapter.js';
+import { FILE_FLAG, isDataFile, isUrl, modifierValue, splitModifier, } from './parseArgv.js';
 /**
- * A command-line file as a JBrowse location: a URL (http, s3, ftp, …) is a
- * `uri`, anything else a local path.
+ * A command-line file as a JBrowse location: a URL is a `uri`, anything else a
+ * local path.
  */
 export function makeLocation(file) {
-    return URL_SCHEME.test(file)
+    return isUrl(file)
         ? { uri: file, locationType: 'UriLocation' }
         : { localPath: file, locationType: 'LocalPathLocation' };
 }
 /**
- * The adapter each typed track flag names. `--bam reads` opens `reads` as BAM
- * whatever its name says, and `--file reads.bam` (or a bare `reads.bam`) types
- * it by name; both build through the add-track format table.
+ * The formats each typed track flag reads, each as the adapters for a plain
+ * file and its bgzipped, tabix-indexed form. `--vcf calls` opens a name that
+ * says none of a flag's formats as its first, `--gff genes.gtf` the format the
+ * name says, and `--bed reads.bam` throws. Both build through the add-track
+ * format table.
  */
-export const trackFlagAdapters = {
-    bam: 'BamAdapter',
-    cram: 'CramAdapter',
-    bigwig: 'BigWigAdapter',
-    vcfgz: 'VcfTabixAdapter',
-    gffgz: 'Gff3TabixAdapter',
-    hic: 'HicAdapter',
-    bigbed: 'BigBedAdapter',
-    bedgz: 'BedTabixAdapter',
+export const trackFlagFormats = {
+    bam: [['BamAdapter']],
+    cram: [['CramAdapter']],
+    bigwig: [['BigWigAdapter']],
+    bigbed: [['BigBedAdapter']],
+    hic: [['HicAdapter']],
+    vcf: [['VcfAdapter', 'VcfTabixAdapter']],
+    gff: [
+        ['Gff3Adapter', 'Gff3TabixAdapter'],
+        ['GtfAdapter', 'GtfTabixAdapter'],
+    ],
+    bed: [
+        ['BedAdapter', 'BedTabixAdapter'],
+        ['BedGraphAdapter', 'BedGraphTabixAdapter'],
+        ['BedpeAdapter'],
+    ],
 };
-export const trackFlags = Object.keys(trackFlagAdapters);
-function isTrackFlag(flag) {
-    return flag in trackFlagAdapters;
+export const trackFlags = Object.keys(trackFlagFormats);
+export function isTrackFlag(flag) {
+    return Object.hasOwn(trackFlagFormats, flag);
+}
+/** The flags that open a genome file. */
+export const genomeFlags = ['fasta', 'chromSizes'];
+export function isGenomeFlag(flag) {
+    return genomeFlags.includes(flag);
+}
+const allFormats = trackFlags.flatMap(flag => trackFlagFormats[flag]);
+function formatOf(formats, adapterType) {
+    return formats.find(format => format.includes(adapterType));
+}
+// The format the name says, or a typed flag's first for a name that says none
+// of the track flags' formats; then its tabix adapter for a `.gz` name or a
+// named index. Undefined leaves a bare file to the adapter its name says.
+function chosenAdapterType(flag, file, index) {
+    const byName = adapterTypeByName(file) ?? '';
+    const own = isTrackFlag(flag) ? trackFlagFormats[flag] : allFormats;
+    const other = trackFlags.find(f => f !== flag && formatOf(trackFlagFormats[f], byName));
+    if (isTrackFlag(flag) && !formatOf(own, byName) && other) {
+        throw new Error(`--${flag} ${file}: its name says a ${other} file, which --${flag} does not read; pass it bare or as --${other}`);
+    }
+    const format = formatOf(own, byName) ?? (isTrackFlag(flag) ? own[0] : undefined);
+    const tabix = !!index || /\.b?gz$/i.test(file);
+    return format && (format[tabix ? 1 : 0] ?? format[0]);
 }
 const SEQUENCE_TRACK = 'ReferenceSequenceTrack';
 /**
@@ -37,7 +68,7 @@ const SEQUENCE_TRACK = 'ReferenceSequenceTrack';
  * for a file the format table cannot type, naming the flags that would.
  */
 export function fileAdapter(file, { adapterType, index } = {}) {
-    const { adapter } = guessTrack({
+    const { adapter, files } = guessTrack({
         location: file,
         index,
         adapterType,
@@ -46,10 +77,13 @@ export function fileAdapter(file, { adapterType, index } = {}) {
     if (adapter.type === 'UNKNOWN' || adapter.type === 'UNSUPPORTED') {
         throw new Error(`JBrowse cannot tell what kind of file ${file} is from its name. Name its type with a flag: ${trackFlags.map(f => `--${f}`).join(', ')}`);
     }
+    else if (index && !files.includes(index)) {
+        throw new Error(`${file} opens with ${adapter.type}, which reads no index, so index:${index} applies to nothing`);
+    }
     return adapter;
 }
-export function isSequenceAdapter(adapter) {
-    return guessTrackType(adapter.type) === SEQUENCE_TRACK;
+export function isSequenceAdapter({ type }) {
+    return guessTrackType(type) === SEQUENCE_TRACK;
 }
 /**
  * An assembly from a sequence file's adapter, named after the file, with the
@@ -57,7 +91,7 @@ export function isSequenceAdapter(adapter) {
  */
 export function sequenceAssembly(adapter, file, { aliases, cytobands, trackId = 'refseq', } = {}) {
     return {
-        name: path.basename(file).replace(/\.(chrom\.)?sizes$/i, ''),
+        name: fileNameOf(file).replace(/\.(chrom\.)?sizes$/i, ''),
         sequence: { type: SEQUENCE_TRACK, trackId, adapter },
         ...(aliases
             ? {
@@ -81,6 +115,37 @@ export function sequenceAssembly(adapter, file, { aliases, cytobands, trackId =
             : {}),
     };
 }
+const GENOME_MODIFIERS = new Set(['aliases', 'cytobands']);
+/**
+ * The assembly a genome argument opens, `--fasta ref.fa`, `--chromSizes
+ * a.sizes` or a bare genome file, with the files its `aliases:` and
+ * `cytobands:` modifiers name. `--fasta` opens a name the format table does not
+ * know as an indexed FASTA. `unused` is the modifiers it has no use for, for
+ * the caller to report.
+ */
+export function genomeAssembly(flag, [file, ...mods], trackId) {
+    if (!file) {
+        throw new Error(`--${flag} requires a file argument`);
+    }
+    const adapter = fileAdapter(file, {
+        adapterType: flag === 'chromSizes'
+            ? 'ChromSizesAdapter'
+            : flag === 'fasta' && !isDataFile(file)
+                ? 'IndexedFastaAdapter'
+                : undefined,
+    });
+    if (!isSequenceAdapter(adapter)) {
+        throw new Error(`--${flag} ${file} is not a genome: a FASTA, 2bit or .chrom.sizes file`);
+    }
+    return {
+        assembly: sequenceAssembly(adapter, file, {
+            aliases: modifierValue(mods, 'aliases'),
+            cytobands: modifierValue(mods, 'cytobands'),
+            trackId,
+        }),
+        unused: mods.filter(mod => !GENOME_MODIFIERS.has(splitModifier(mod)?.[0] ?? '')),
+    };
+}
 /**
  * A track for one file argument, labelled by `name:` or the file's basename.
  * Without `assemblyName` it names no assembly, for a caller that learns the
@@ -93,17 +158,18 @@ export function fileTrack(flag, [file, ...mods], assemblyName) {
     if (!isTrackFlag(flag) && flag !== FILE_FLAG) {
         throw new Error(`--${flag} is not a file flag`);
     }
+    const index = modifierValue(mods, 'index');
     const adapter = fileAdapter(file, {
-        adapterType: isTrackFlag(flag) ? trackFlagAdapters[flag] : undefined,
-        index: modifierValue(mods, 'index'),
+        adapterType: chosenAdapterType(flag, file, index),
+        index,
     });
     if (isSequenceAdapter(adapter)) {
         throw new Error(`${file} is a genome, and this view already has one; open one genome per view`);
     }
     return {
         type: guessTrackType(adapter.type, file),
-        trackId: path.basename(file),
-        name: modifierValue(mods, 'name') ?? path.basename(file),
+        trackId: fileNameOf(file),
+        name: modifierValue(mods, 'name') ?? fileNameOf(file),
         ...(assemblyName ? { assemblyNames: [assemblyName] } : {}),
         adapter,
     };

package/esm/hostedGenomes.d.ts

@@ -0,0 +1,39 @@
+import type { ComparativeRow } from './comparative.ts';
+import type { Track } from './fileInput.ts';
+type NamedAssembly = {
+    name: string;
+} & Record<string, unknown>;
+export interface TextSearchAdapter {
+    type: string;
+    assemblyNames?: string[];
+    [key: string]: unknown;
+}
+/**
+ * The parts of a genomes.jbrowse.org config.json a comparative view reads, with
+ * the assembly type the caller holds them as.
+ */
+export interface HostedConfig<A extends {
+    name: string;
+} = NamedAssembly> {
+    assemblies?: A[];
+    tracks?: Track[];
+    aggregateTextSearchAdapters?: TextSearchAdapter[];
+}
+/**
+ * What a comparative view's `--genome` rows take from their hosted configs,
+ * keyed by genome name: each genome's assembly, its gene-name search, so a row's
+ * `loc:` can name a gene, and a comparison for each gap beside a hosted row
+ * that no comparison file fills.
+ *
+ * A config holds the comparisons its genome is the target of, so a pair is
+ * often hosted twice, once in each direction; the upper row's config wins, and
+ * the gap draws one comparison. A gap neither config covers throws.
+ */
+export declare function hostedComparative<A extends {
+    name: string;
+}>(rows: ComparativeRow[], fileTracks: Track[], configs: ReadonlyMap<string, HostedConfig<A>>): {
+    assemblies: A[];
+    textSearchAdapters: TextSearchAdapter[];
+    tracks: Track[];
+};
+export {};

package/esm/hostedGenomes.js

@@ -0,0 +1,45 @@
+// order-free, as a track's [query, target] follows its file format; a self
+// pair names the assembly twice
+function compares(track, a, b) {
+    const names = track.assemblyNames ?? [];
+    return a === b
+        ? names.filter(name => name === a).length >= 2
+        : names.includes(a) && names.includes(b);
+}
+/**
+ * What a comparative view's `--genome` rows take from their hosted configs,
+ * keyed by genome name: each genome's assembly, its gene-name search, so a row's
+ * `loc:` can name a gene, and a comparison for each gap beside a hosted row
+ * that no comparison file fills.
+ *
+ * A config holds the comparisons its genome is the target of, so a pair is
+ * often hosted twice, once in each direction; the upper row's config wins, and
+ * the gap draws one comparison. A gap neither config covers throws.
+ */
+export function hostedComparative(rows, fileTracks, configs) {
+    const assemblies = [...configs].map(([name, config]) => {
+        const assembly = config.assemblies?.find(a => a.name === name);
+        if (!assembly) {
+            throw new Error(`--genome ${name}: its hosted config names no assembly ${name}`);
+        }
+        return assembly;
+    });
+    const textSearchAdapters = [...configs].flatMap(([name, config]) => (config.aggregateTextSearchAdapters ?? []).filter(adapter => adapter.assemblyNames?.includes(name)));
+    const tracks = [];
+    for (const [i, lower] of rows.slice(1).entries()) {
+        const a = rows[i].assembly;
+        const b = lower.assembly;
+        const sources = [configs.get(a), configs.get(b)].filter(c => !!c);
+        if (sources.length &&
+            ![...fileTracks, ...tracks].some(track => compares(track, a, b))) {
+            const hosted = sources
+                .flatMap(config => config.tracks ?? [])
+                .find(track => track.type === 'SyntenyTrack' && compares(track, a, b));
+            if (!hosted) {
+                throw new Error(`genomes.jbrowse.org has no comparison between ${a} and ${b}; put a comparison file between them`);
+            }
+            tracks.push(hosted);
+        }
+    }
+    return { assemblies, textSearchAdapters, tracks };
+}

package/esm/index.d.ts

@@ -1,6 +1,10 @@
-export { type Adapter, type Location, guessTrack, guessTrackType, makeLocationProtocol, siblingSidecar, syntenyAdapterTypes, } from './fileAdapter.ts';
-export { type Assembly, type Track, type TrackFlag, fileAdapter, fileTrack, isSequenceAdapter, makeLocation, sequenceAssembly, trackFlagAdapters, trackFlags, } from './fileInput.ts';
+export { type Adapter, type Location, guessTrack, guessTrackType, makeLocationProtocol, syntenyAdapterTypes, } from './fileAdapter.ts';
+export { type Assembly, type Track, type TrackFlag, fileAdapter, fileTrack, genomeAssembly, genomeFlags, isGenomeFlag, makeLocation, trackFlags, } from './fileInput.ts';
 export { genomeConfigUrl } from './genome.ts';
+export { type HostedConfig, hostedComparative } from './hostedGenomes.ts';
+export { mergeSettings, viewSettings } from './slotPath.ts';
+export { parseBool } from './modifierValues.ts';
 export { resolveTrackId, trackMatches, trackName, trackType, } from './trackIds.ts';
-export { type LaunchPlan, launchFlags, launchPlan } from './launchPlan.ts';
-export { type Entry, FILE_FLAG, isDataFile, isModifier, modifierValue, parseArgv, splitModifier, standardizeArgv, } from './parseArgv.ts';
+export { type ComparativeData, type ComparativeRow, type SyntenyFlag, buildComparative, comparativeRole, hasComparativeArgs, syntenyFlags, } from './comparative.ts';
+export { type ComparativeLaunchPlan, type LaunchPlan, type LaunchViewType, type LinearLaunchPlan, type ShowTrack, exportBooleanFlags, launchFlags, launchPlan, launchViewType, takesFile, uniqueId, } from './launchPlan.ts';
+export { type Entry, FILE_FLAG, isDataFile, isModifier, isUrl, modifierValue, parseArgv, standardizeArgv, } from './parseArgv.ts';

package/esm/index.js

@@ -1,6 +1,10 @@
-export { guessTrack, guessTrackType, makeLocationProtocol, siblingSidecar, syntenyAdapterTypes, } from './fileAdapter.js';
-export { fileAdapter, fileTrack, isSequenceAdapter, makeLocation, sequenceAssembly, trackFlagAdapters, trackFlags, } from './fileInput.js';
+export { guessTrack, guessTrackType, makeLocationProtocol, syntenyAdapterTypes, } from './fileAdapter.js';
+export { fileAdapter, fileTrack, genomeAssembly, genomeFlags, isGenomeFlag, makeLocation, trackFlags, } from './fileInput.js';
 export { genomeConfigUrl } from './genome.js';
+export { hostedComparative } from './hostedGenomes.js';
+export { mergeSettings, viewSettings } from './slotPath.js';
+export { parseBool } from './modifierValues.js';
 export { resolveTrackId, trackMatches, trackName, trackType, } from './trackIds.js';
-export { launchFlags, launchPlan } from './launchPlan.js';
-export { FILE_FLAG, isDataFile, isModifier, modifierValue, parseArgv, splitModifier, standardizeArgv, } from './parseArgv.js';
+export { buildComparative, comparativeRole, hasComparativeArgs, syntenyFlags, } from './comparative.js';
+export { exportBooleanFlags, launchFlags, launchPlan, launchViewType, takesFile, uniqueId, } from './launchPlan.js';
+export { FILE_FLAG, isDataFile, isModifier, isUrl, modifierValue, parseArgv, standardizeArgv, } from './parseArgv.js';

package/esm/launchPlan.d.ts

@@ -1,11 +1,30 @@
 import type { Assembly, Track } from './fileInput.ts';
 import type { Entry } from './parseArgv.ts';
 /**
- * What a command line asks a JBrowse app to open: a genome, the files and
- * tracks to show on it, and where. Plain JSON, so it can cross from the process
- * that read the files to the one that draws them.
+ * The views jb2export's subcommand words name, which Desktop takes as its
+ * first argument too.
  */
-export interface LaunchPlan {
+export declare const launchViewTypes: {
+    readonly lgv: 'LinearGenomeView';
+    readonly synteny: 'LinearSyntenyView';
+    readonly dotplot: 'DotplotView';
+};
+export type LaunchViewType = (typeof launchViewTypes)[keyof typeof launchViewTypes];
+export declare function launchViewType(word: string): LaunchViewType | undefined;
+/**
+ * What a command line asks a JBrowse app to open: genomes, the files and
+ * tracks to show on them, and where. Plain JSON, so it can cross from the
+ * process that read the files to the one that draws them.
+ */
+export type LaunchPlan = LinearLaunchPlan | ComparativeLaunchPlan;
+interface PlanBase {
+    /** settings `--view` writes on the view, as a session spec's view holds them */
+    view: Record<string, unknown>;
+    /** modifiers this plan does not carry into the view, for the app to report */
+    unapplied: string[];
+}
+export interface LinearLaunchPlan extends PlanBase {
+    type: 'LinearGenomeView';
     /** a config.json path or URL to load first: `--genome`'s hosted one, or `--config` */
     config?: string;
     /** a genome built from a file, which no config then supplies */
@@ -18,15 +37,60 @@ export interface LaunchPlan {
      * config's, which only the app that fetches it can name.
      */
     tracks: Track[];
-    /** trackIds to show, files' and `--track`'s, in command-line order */
-    show: string[];
-    /** modifiers this plan does not carry into the view, for the app to report */
-    unapplied: string[];
+    /**
+     * The tracks to show, files' and `--track`'s, in command-line order, each
+     * with the modifiers the app applies once it knows the track's display
+     */
+    show: ShowTrack[];
+}
+/** A synteny view or dotplot of genome files and hosted genomes. */
+export interface ComparativeLaunchPlan extends PlanBase {
+    type: 'LinearSyntenyView' | 'DotplotView';
+    /** the genomes built from files */
+    assemblies: Assembly[];
+    /**
+     * each `--genome` and its hosted config, which the app fetches and hands to
+     * `hostedComparative`
+     */
+    hosted: {
+        name: string;
+        config: string;
+    }[];
+    /**
+     * one row per genome, as a session spec's comparative view lists them; the
+     * top row is a dotplot's x axis
+     */
+    views: {
+        assembly: string;
+        loc?: string;
+    }[];
+    /** the comparison files' tracks, each between the genomes it compares */
+    tracks: Track[];
+}
+export interface ShowTrack {
+    trackId: string;
+    modifiers: string[];
 }
 export declare const launchFlags: ReadonlySet<string>;
+/**
+ * jb2export's flags that take only true or false, so a file after one is a
+ * file of its own. Desktop reads them to report one without taking the file.
+ */
+export declare const exportBooleanFlags: ReadonlySet<string>;
+/** Whether a flag opens a data file, as a track, genome or comparison flag does. */
+export declare function takesFile(key: string): boolean;
+/**
+ * `base`, or the first of `base-2`, `base-3`, ... that `used` lacks, which it
+ * adds to `used`.
+ */
+export declare function uniqueId(used: Set<string>, base: string): string;
 /**
  * The plan a command line describes, with every local path resolved against
  * `cwd`: the directory the command ran in, which is not the app's own once a
  * second launch hands its arguments to a running one.
+ *
+ * `viewType` is the view a subcommand word named. Without one, a second genome
+ * or a comparison file opens a synteny view, and anything else a linear one.
  */
-export declare function launchPlan(entries: Entry[], cwd: string): LaunchPlan;
+export declare function launchPlan(entries: Entry[], cwd: string, viewType?: LaunchViewType): LaunchPlan;
+export {};