@jbrowse/bandage-core 7.2.0 → 7.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/chunks/{chunk-MH5IA57M.js → chunk-36UKA6RQ.js} +1 -1
- package/dist/chunks/{chunk-QMJ4J5PT.js → chunk-45J7P6YW.js} +36 -37
- package/dist/chunks/{chunk-EXSXBIMH.js → chunk-5N5YRRFE.js} +1 -1
- package/dist/chunks/{chunk-E7FWQQHP.js → chunk-7GBL7SJY.js} +15 -4
- package/dist/chunks/{chunk-Y7UR3MDE.js → chunk-AGJZ5RDC.js} +1 -1
- package/dist/chunks/{chunk-4FQTTG5F.js → chunk-AYOSNXLQ.js} +1 -1
- package/dist/chunks/{chunk-TQ7VCGJR.js → chunk-C4IUUTAB.js} +1 -1
- package/dist/chunks/chunk-CBBDB3UC.js +27 -0
- package/dist/chunks/{chunk-S73EYTZA.js → chunk-ERHAGG72.js} +1 -1
- package/dist/chunks/{chunk-KREASK3Z.js → chunk-HPIZNWF7.js} +4 -4
- package/dist/chunks/{chunk-JKXE6CIP.js → chunk-IW6K4VHZ.js} +4 -4
- package/dist/chunks/chunk-K5SIJGAE.js +12 -0
- package/dist/chunks/{chunk-CNQSHEBS.js → chunk-O7QXUXGZ.js} +1 -1
- package/dist/chunks/{chunk-UGD6ZMOF.js → chunk-RCPGXIWA.js} +6 -7
- package/dist/chunks/{chunk-EPWYRSHH.js → chunk-SGAMPIKO.js} +22 -0
- package/dist/chunks/{chunk-VST5SR4C.js → chunk-W7R55CIZ.js} +1 -1
- package/dist/chunks/{chunk-VECR253P.js → chunk-Z3OHBOEA.js} +1 -1
- package/dist/cli/figure.js +47 -58
- package/dist/figure.js +24 -24
- package/dist/figureSettings.js +25 -0
- package/dist/index.js +122 -106
- package/dist/layout/tubeMapLayout.js +4 -4
- package/dist/layout/walkRowDraw.js +8 -8
- package/dist/layout/walkRowLayout.js +1 -1
- package/dist/layout/walkStrip.js +9 -9
- package/dist/layoutModes.js +8 -8
- package/dist/layoutQualities.js +6 -0
- package/dist/pathColors.js +7 -5
- package/dist/pipeline.js +6 -2
- package/dist/referenceRampCss.js +6 -6
- package/dist/referenceStrip.js +6 -6
- package/dist/renderer/GeometryBuilder.js +5 -5
- package/dist/tubeMap/coarsen.js +5 -5
- package/dist/tubeMap/nodeColors.js +6 -6
- package/dist/types/figure.d.ts +1 -0
- package/dist/types/figureSettings.d.ts +15 -0
- package/dist/types/index.d.ts +6 -1
- package/dist/types/layoutQualities.d.ts +17 -0
- package/dist/types/pathColors.d.ts +4 -0
- package/dist/types/pipeline.d.ts +2 -0
- package/dist/types/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/viewport.js +3 -3
- package/dist/walkEncoding.js +6 -6
- package/dist/walkHighlight.js +7 -7
- package/package.json +1 -1
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import {
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stripGeneGaps,
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walkStripFrame,
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walkStripLabelsTree
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Canvas2DRenderer
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svgCanvas
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stripGeneGaps,
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walkStripFrame,
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walkStripLabelsTree
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} from "./chunk-KREASK3Z.js";
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import {
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walkRowsKey,
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walkRowsKeyTree,
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walkRowsTree
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} from "./chunk-
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} from "./chunk-RCPGXIWA.js";
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import {
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EXON_COLOR,
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exonOutlineTree,
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genePins
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version
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axisScaleOf
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import {
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facetLifts,
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walkLift
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encodingStops
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} from "./chunk-TQ7VCGJR.js";
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} from "./chunk-36UKA6RQ.js";
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rangeText,
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walkKey
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version
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} from "./chunk-ERHAGG72.js";
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import {
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axisScaleOf
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} from "./chunk-AGJZ5RDC.js";
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import {
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encodingStops
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} from "./chunk-C4IUUTAB.js";
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import {
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buildGeometry,
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computeReferenceRamp
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} from "./chunk-
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} from "./chunk-W7R55CIZ.js";
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nodeInk
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} from "./chunk-PBENCR5L.js";
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import {
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referenceLabel
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} from "./chunk-RAKOB6IV.js";
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geneLabelCandidates
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walkRowsExtent
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pathLegend
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pathLegend,
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walkLabelsOf
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} from "./chunk-7GBL7SJY.js";
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import {
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deletionDrawing,
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deletionEdges
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serializeEl
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FIT_PADDING,
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drawingBounds,
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fitTransform
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deletionDrawing,
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deletionEdges
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// src/figure.ts
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var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';
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const lift = layers.length > 0 && !layout.tubeMap ? walkLift(graph, layers, walkRamp) : void 0;
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const facet = facetSettingOf(o.facet);
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const panels = facet.field && lift && lift.walks.length > 1 ? facetLifts(graph, lift, layers, walkRamp) : void 0;
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graph.paths?.length ? pathLegend(graph.paths) : []
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const labelOf = (name) => labels.get(name) ?? name;
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const referenceName = o.referenceName ?? referenceLabel(graph, region);
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function coalesceRuns(runs, pxPerBp) {
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|
}
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|
return graph;
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engine: "fmmm",
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quality: 2,
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linearLayout: false,
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bubbleSpread: "auto",
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spacing: 1,
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};
|
|
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function engineSettingsOf(s = {}) {
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componentSeparation: s.componentSeparation ?? ENGINE_DEFAULTS.componentSeparation,
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showDeletionEdges: s.showDeletionEdges ?? ENGINE_DEFAULTS.showDeletionEdges
|
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|
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|
var COMPONENT_SEPARATION = 15;
|
|
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|
function engineRequest(graph, scaling, settings) {
|
|
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79
|
const anchored = graph.nodes.some(isBackbone);
|
|
@@ -210,6 +230,8 @@ function drawingBounds(layout, opts = {}) {
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export {
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|
package/dist/cli/figure.js
CHANGED
|
@@ -4,6 +4,15 @@ import {
|
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|
genesFromGff3Lines,
|
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genesFromText
|
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} from "../chunks/chunk-BXEPA4KS.js";
|
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import {
|
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HPRC_GBZ,
|
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cutGbzRegion,
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openGbz,
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parseRegion
|
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} from "../chunks/chunk-73RSLGZT.js";
|
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import "../chunks/chunk-LTUWJKHD.js";
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|
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import "../chunks/chunk-WSIFAZU7.js";
|
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|
import {
|
|
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17
|
LAYOUT_ENGINE_VALUES,
|
|
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18
|
isLayoutEngineKind,
|
|
@@ -11,89 +20,81 @@ import {
|
|
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20
|
} from "../chunks/chunk-6EJIU6IA.js";
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|
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+
import "../chunks/chunk-7XHHVYG7.js";
|
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import {
|
|
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25
|
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|
|
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|
layoutModeByValue
|
|
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|
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} from "../chunks/chunk-
|
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|
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import "../chunks/chunk-4FQTTG5F.js";
|
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|
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import "../chunks/chunk-TEDQJPMI.js";
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|
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} from "../chunks/chunk-IW6K4VHZ.js";
|
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|
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|
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|
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import "../chunks/chunk-C44YRP5F.js";
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|
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import "../chunks/chunk-7XHHVYG7.js";
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|
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|
|
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|
figureSvg
|
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|
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} from "../chunks/chunk-
|
|
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|
+
} from "../chunks/chunk-45J7P6YW.js";
|
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|
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|
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|
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import "../chunks/chunk-KREASK3Z.js";
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|
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|
|
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|
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|
|
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45
|
placeRowGenes
|
|
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|
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} from "../chunks/chunk-
|
|
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|
+
} from "../chunks/chunk-RCPGXIWA.js";
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|
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import "../chunks/chunk-
|
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|
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import "../chunks/chunk-Y7UR3MDE.js";
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|
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import "../chunks/chunk-MH5IA57M.js";
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|
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import "../chunks/chunk-TQ7VCGJR.js";
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|
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import "../chunks/chunk-36UKA6RQ.js";
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|
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import
|
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|
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|
|
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|
-
|
|
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|
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|
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|
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import "../chunks/chunk-
|
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|
-
import "../chunks/chunk-IGVV37VI.js";
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import "../chunks/chunk-72N5DJHZ.js";
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import "../chunks/chunk-QYBZZI5H.js";
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import "../chunks/chunk-CDLPYR5O.js";
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|
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import "../chunks/chunk-VECR253P.js";
|
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|
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import "../chunks/chunk-VST5SR4C.js";
|
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|
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import "../chunks/chunk-Z3OHBOEA.js";
|
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|
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import "../chunks/chunk-ERHAGG72.js";
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|
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import "../chunks/chunk-AGJZ5RDC.js";
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|
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import "../chunks/chunk-C4IUUTAB.js";
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|
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|
+
import "../chunks/chunk-W7R55CIZ.js";
|
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56
|
import "../chunks/chunk-UMNCCYBN.js";
|
|
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|
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|
|
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|
+
import {
|
|
59
|
+
featuresOnBackbone,
|
|
60
|
+
graphBackbone,
|
|
61
|
+
refNameBinding
|
|
62
|
+
} from "../chunks/chunk-RAKOB6IV.js";
|
|
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|
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|
|
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64
|
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|
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|
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|
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|
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|
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import "../chunks/chunk-JVLURPFW.js";
|
|
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67
|
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|
|
64
68
|
import {
|
|
65
69
|
filterSamples,
|
|
66
70
|
walkRows
|
|
67
71
|
} from "../chunks/chunk-SZNZ2T6D.js";
|
|
68
|
-
import "../chunks/chunk-
|
|
69
|
-
import "../chunks/chunk-ES2N6V56.js";
|
|
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|
-
import "../chunks/chunk-ST2IBUAN.js";
|
|
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|
+
import "../chunks/chunk-7GBL7SJY.js";
|
|
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73
|
import "../chunks/chunk-3ZZSX5HN.js";
|
|
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74
|
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|
|
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|
+
import "../chunks/chunk-JKJWSY4V.js";
|
|
76
|
+
import "../chunks/chunk-NNODIW4U.js";
|
|
77
|
+
import "../chunks/chunk-6SBUFFTB.js";
|
|
78
|
+
import {
|
|
79
|
+
engineSettingsOf,
|
|
80
|
+
forceLayout,
|
|
81
|
+
loadGraph
|
|
82
|
+
} from "../chunks/chunk-SGAMPIKO.js";
|
|
83
|
+
import "../chunks/chunk-PUG7LXDF.js";
|
|
84
|
+
import "../chunks/chunk-IGVV37VI.js";
|
|
85
|
+
import "../chunks/chunk-72N5DJHZ.js";
|
|
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|
+
import "../chunks/chunk-QYBZZI5H.js";
|
|
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|
+
import "../chunks/chunk-CDLPYR5O.js";
|
|
88
|
+
import "../chunks/chunk-JVLURPFW.js";
|
|
89
|
+
import "../chunks/chunk-ES2N6V56.js";
|
|
90
|
+
import "../chunks/chunk-ST2IBUAN.js";
|
|
91
|
+
import "../chunks/chunk-BPLIXMH7.js";
|
|
73
92
|
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|
|
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93
|
import "../chunks/chunk-UVBGRJQX.js";
|
|
75
94
|
import "../chunks/chunk-6JEWNXCQ.js";
|
|
76
|
-
import "../chunks/chunk-JKJWSY4V.js";
|
|
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95
|
import "../chunks/chunk-N6FECAXP.js";
|
|
78
96
|
import "../chunks/chunk-2CVHXFK7.js";
|
|
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97
|
import "../chunks/chunk-CPMHA4W5.js";
|
|
80
|
-
import "../chunks/chunk-NNODIW4U.js";
|
|
81
|
-
import "../chunks/chunk-6SBUFFTB.js";
|
|
82
|
-
import {
|
|
83
|
-
HPRC_GBZ,
|
|
84
|
-
cutGbzRegion,
|
|
85
|
-
haplotypeIndexBeside,
|
|
86
|
-
openGbz,
|
|
87
|
-
parseRegion
|
|
88
|
-
} from "../chunks/chunk-73RSLGZT.js";
|
|
89
|
-
import "../chunks/chunk-LTUWJKHD.js";
|
|
90
|
-
import "../chunks/chunk-WSIFAZU7.js";
|
|
91
|
-
import {
|
|
92
|
-
featuresOnBackbone,
|
|
93
|
-
graphBackbone,
|
|
94
|
-
refNameBinding
|
|
95
|
-
} from "../chunks/chunk-RAKOB6IV.js";
|
|
96
|
-
import "../chunks/chunk-BPLIXMH7.js";
|
|
97
98
|
import "../chunks/chunk-FYQWPEEY.js";
|
|
98
99
|
|
|
99
100
|
// src/cli/figure.ts
|
|
@@ -241,19 +242,7 @@ async function renderSpec(spec, base) {
|
|
|
241
242
|
const graph = loadGraph(source.text, source.name, {
|
|
242
243
|
referencePath: spec.referencePath
|
|
243
244
|
});
|
|
244
|
-
const layout = layoutModeByValue(spec.layout ?? "force").run(graph, source.region) ?? (await forceLayout(
|
|
245
|
-
graph,
|
|
246
|
-
{
|
|
247
|
-
quality: spec.quality ?? 2,
|
|
248
|
-
linearLayout: false,
|
|
249
|
-
bubbleSpread: spec.bubbleSpread ?? "auto",
|
|
250
|
-
engine: spec.engine,
|
|
251
|
-
spacing: spec.spacing,
|
|
252
|
-
componentSeparation: spec.componentSeparation,
|
|
253
|
-
showDeletionEdges: spec.showDeletionEdges
|
|
254
|
-
},
|
|
255
|
-
layoutEngine
|
|
256
|
-
)).result;
|
|
245
|
+
const layout = layoutModeByValue(spec.layout ?? "force").run(graph, source.region) ?? (await forceLayout(graph, engineSettingsOf(spec), layoutEngine)).result;
|
|
257
246
|
const bars = spec.walkStrip ? walkRows(graph, source.region) : void 0;
|
|
258
247
|
const stripRows = bars && {
|
|
259
248
|
...bars,
|
package/dist/figure.js
CHANGED
|
@@ -1,51 +1,51 @@
|
|
|
1
1
|
import {
|
|
2
2
|
figureSvg
|
|
3
|
-
} from "./chunks/chunk-
|
|
3
|
+
} from "./chunks/chunk-45J7P6YW.js";
|
|
4
|
+
import "./chunks/chunk-HPIZNWF7.js";
|
|
4
5
|
import "./chunks/chunk-CH3DLBUT.js";
|
|
5
6
|
import "./chunks/chunk-4BYTEJGW.js";
|
|
6
7
|
import "./chunks/chunk-47DYCZOK.js";
|
|
7
|
-
import "./chunks/chunk-
|
|
8
|
-
import "./chunks/chunk-UGD6ZMOF.js";
|
|
8
|
+
import "./chunks/chunk-RCPGXIWA.js";
|
|
9
9
|
import "./chunks/chunk-3S3YVOJ7.js";
|
|
10
10
|
import "./chunks/chunk-BUBZ32IC.js";
|
|
11
|
-
import "./chunks/chunk-
|
|
12
|
-
import "./chunks/chunk-Y7UR3MDE.js";
|
|
13
|
-
import "./chunks/chunk-MH5IA57M.js";
|
|
14
|
-
import "./chunks/chunk-TQ7VCGJR.js";
|
|
11
|
+
import "./chunks/chunk-36UKA6RQ.js";
|
|
15
12
|
import "./chunks/chunk-2LQ5BWT7.js";
|
|
16
|
-
import "./chunks/chunk-
|
|
17
|
-
import "./chunks/chunk-
|
|
18
|
-
import "./chunks/chunk-
|
|
19
|
-
import "./chunks/chunk-
|
|
20
|
-
import "./chunks/chunk-
|
|
21
|
-
import "./chunks/chunk-CDLPYR5O.js";
|
|
22
|
-
import "./chunks/chunk-VECR253P.js";
|
|
23
|
-
import "./chunks/chunk-VST5SR4C.js";
|
|
13
|
+
import "./chunks/chunk-Z3OHBOEA.js";
|
|
14
|
+
import "./chunks/chunk-ERHAGG72.js";
|
|
15
|
+
import "./chunks/chunk-AGJZ5RDC.js";
|
|
16
|
+
import "./chunks/chunk-C4IUUTAB.js";
|
|
17
|
+
import "./chunks/chunk-W7R55CIZ.js";
|
|
24
18
|
import "./chunks/chunk-UMNCCYBN.js";
|
|
25
19
|
import "./chunks/chunk-PBENCR5L.js";
|
|
20
|
+
import "./chunks/chunk-RAKOB6IV.js";
|
|
26
21
|
import "./chunks/chunk-GJMC3PGM.js";
|
|
27
22
|
import "./chunks/chunk-FP4H7SFT.js";
|
|
28
23
|
import "./chunks/chunk-MLSWIMZO.js";
|
|
29
24
|
import "./chunks/chunk-WFB5TXRA.js";
|
|
30
|
-
import "./chunks/chunk-JVLURPFW.js";
|
|
31
25
|
import "./chunks/chunk-3JANT2SW.js";
|
|
32
26
|
import "./chunks/chunk-SZNZ2T6D.js";
|
|
33
|
-
import "./chunks/chunk-
|
|
34
|
-
import "./chunks/chunk-ES2N6V56.js";
|
|
35
|
-
import "./chunks/chunk-ST2IBUAN.js";
|
|
27
|
+
import "./chunks/chunk-7GBL7SJY.js";
|
|
36
28
|
import "./chunks/chunk-3ZZSX5HN.js";
|
|
37
29
|
import "./chunks/chunk-AB35TJST.js";
|
|
30
|
+
import "./chunks/chunk-JKJWSY4V.js";
|
|
31
|
+
import "./chunks/chunk-NNODIW4U.js";
|
|
32
|
+
import "./chunks/chunk-6SBUFFTB.js";
|
|
33
|
+
import "./chunks/chunk-SGAMPIKO.js";
|
|
34
|
+
import "./chunks/chunk-PUG7LXDF.js";
|
|
35
|
+
import "./chunks/chunk-IGVV37VI.js";
|
|
36
|
+
import "./chunks/chunk-72N5DJHZ.js";
|
|
37
|
+
import "./chunks/chunk-QYBZZI5H.js";
|
|
38
|
+
import "./chunks/chunk-CDLPYR5O.js";
|
|
39
|
+
import "./chunks/chunk-JVLURPFW.js";
|
|
40
|
+
import "./chunks/chunk-ES2N6V56.js";
|
|
41
|
+
import "./chunks/chunk-ST2IBUAN.js";
|
|
42
|
+
import "./chunks/chunk-BPLIXMH7.js";
|
|
38
43
|
import "./chunks/chunk-TAMCZHLW.js";
|
|
39
44
|
import "./chunks/chunk-UVBGRJQX.js";
|
|
40
45
|
import "./chunks/chunk-6JEWNXCQ.js";
|
|
41
|
-
import "./chunks/chunk-JKJWSY4V.js";
|
|
42
46
|
import "./chunks/chunk-N6FECAXP.js";
|
|
43
47
|
import "./chunks/chunk-2CVHXFK7.js";
|
|
44
48
|
import "./chunks/chunk-CPMHA4W5.js";
|
|
45
|
-
import "./chunks/chunk-NNODIW4U.js";
|
|
46
|
-
import "./chunks/chunk-6SBUFFTB.js";
|
|
47
|
-
import "./chunks/chunk-RAKOB6IV.js";
|
|
48
|
-
import "./chunks/chunk-BPLIXMH7.js";
|
|
49
49
|
import "./chunks/chunk-FYQWPEEY.js";
|
|
50
50
|
export {
|
|
51
51
|
figureSvg
|